├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── advanced.rst ├── basic.rst ├── citation.rst ├── conf.py ├── images │ ├── com_0.png │ ├── com_0_155.png │ ├── com_index.png │ ├── example_1.png │ ├── plasmid_cointegrates.png │ ├── russian_dolls_fusion.png │ └── russian_dolls_network.png ├── index.rst ├── installation.rst ├── output.rst ├── requirements.txt ├── tips.rst └── tutorial.rst ├── env.yaml ├── pling ├── __init__.py ├── align_snakemake │ ├── Snakefile │ ├── integerise_plasmids.py │ ├── matches.py │ └── unimog.py ├── batching │ ├── Snakefile │ └── get_batches.py ├── common_rules │ └── common_rules.smk ├── dcj_snakemake │ ├── Snakefile │ ├── __init__.py │ ├── commons.py │ ├── dcj.py │ ├── glpk_and_ding.py │ ├── glpk_sol_to_gurobi_sol.py │ └── gurobi_and_ding.py ├── jac_network_snakemake │ ├── Snakefile │ └── seq_containment.py ├── resources.tsv ├── run_pling.py └── utils.py ├── pyproject.toml ├── setup.py └── tests ├── __init__.py ├── dcj_snakemake ├── __init__.py ├── test_cases │ └── glpk_sol_to_gurobi_sol │ │ ├── test_case_1 │ │ ├── glpk.sol.txt │ │ ├── glpk_to_gurobi.sol.txt │ │ └── gurobi.sol │ │ └── test_case_2 │ │ ├── glpk.sol.txt │ │ ├── glpk_to_gurobi.sol.txt │ │ └── gurobi.sol └── test_glpk_sol_to_gurobi_sol.py ├── integration_test ├── __init__.py ├── data │ ├── .gitignore │ ├── CP057418.1.fna │ ├── NZ_CP027199.1.fna │ ├── NZ_LR882977.1.fna │ ├── NZ_MF510423.1.fna │ ├── all_plasmids_distances.align.truth.tsv │ ├── all_plasmids_distances.anno.truth.tsv │ ├── bakta_db │ │ ├── amrfinderplus-db │ │ │ ├── 2021-09-30.1 │ │ │ │ ├── AMR.LIB.h3f │ │ │ │ ├── AMR.LIB.h3i │ │ │ │ ├── AMR.LIB.h3m │ │ │ │ ├── AMR.LIB.h3p │ │ │ │ ├── AMRProt-mutation.tab │ │ │ │ ├── AMRProt-suppress │ │ │ │ ├── AMRProt-susceptible.tab │ │ │ │ ├── AMRProt.pdb │ │ │ │ ├── AMRProt.phr │ │ │ │ ├── AMRProt.pin │ │ │ │ ├── AMRProt.psq │ │ │ │ ├── AMRProt.ptf │ │ │ │ ├── AMRProt.pto │ │ │ │ ├── AMR_CDS.ndb │ │ │ │ ├── AMR_CDS.nhr │ │ │ │ ├── AMR_CDS.nin │ │ │ │ ├── AMR_CDS.not │ │ │ │ ├── AMR_CDS.nsq │ │ │ │ ├── AMR_CDS.ntf │ │ │ │ ├── AMR_CDS.nto │ │ │ │ ├── database_format_version.txt │ │ │ │ ├── fam.tab │ │ │ │ ├── taxgroup.tab │ │ │ │ └── version.txt │ │ │ └── latest │ │ ├── antifam.h3f │ │ ├── antifam.h3i │ │ ├── antifam.h3m │ │ ├── antifam.h3p │ │ ├── bakta.db │ │ ├── expert-protein-sequences.dmnd │ │ ├── ncRNA-genes.i1f │ │ ├── ncRNA-genes.i1i │ │ ├── ncRNA-genes.i1m │ │ ├── ncRNA-genes.i1p │ │ ├── ncRNA-regions.i1f │ │ ├── ncRNA-regions.i1i │ │ ├── ncRNA-regions.i1m │ │ ├── ncRNA-regions.i1p │ │ ├── oric.fna │ │ ├── orit.fna │ │ ├── pfam.h3f │ │ ├── pfam.h3i │ │ ├── pfam.h3m │ │ ├── pfam.h3p │ │ ├── psc.dmnd │ │ ├── rRNA.i1f │ │ ├── rRNA.i1i │ │ ├── rRNA.i1m │ │ ├── rRNA.i1p │ │ ├── rfam-go.tsv │ │ ├── sorf.dmnd │ │ └── version.json │ └── incy_list_4.txt └── test_integration_test.py ├── unimog_tests ├── __init__.py ├── test_cases │ ├── git_issues │ │ ├── containment_1 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── all_plasmids_distances.tsv │ │ │ │ ├── batches │ │ │ │ ├── .snakemake_timestamp │ │ │ │ ├── batch_0.txt │ │ │ │ ├── batch_1.txt │ │ │ │ ├── batch_10.txt │ │ │ │ ├── batch_2.txt │ │ │ │ ├── batch_3.txt │ │ │ │ ├── batch_4.txt │ │ │ │ ├── batch_5.txt │ │ │ │ ├── batch_6.txt │ │ │ │ ├── batch_7.txt │ │ │ │ ├── batch_8.txt │ │ │ │ ├── batch_9.txt │ │ │ │ └── batching_info.txt │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ ├── containment_communities │ │ │ │ │ ├── .snakemake_timestamp │ │ │ │ │ ├── objects │ │ │ │ │ │ ├── communities.pkl │ │ │ │ │ │ ├── communities.tsv │ │ │ │ │ │ ├── communities.txt │ │ │ │ │ │ └── plasmid_graph.pkl │ │ │ │ │ └── visualisations │ │ │ │ │ │ ├── communities │ │ │ │ │ │ ├── graphs │ │ │ │ │ │ │ └── community_0.html │ │ │ │ │ │ ├── index.html │ │ │ │ │ │ └── libs │ │ │ │ │ │ │ ├── bluebird.js │ │ │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ │ │ ├── resources │ │ │ │ │ │ │ └── images │ │ │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ │ │ └── style.css │ │ │ │ │ │ └── single_graph │ │ │ │ │ │ ├── libs │ │ │ │ │ │ ├── bluebird.js │ │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ │ ├── resources │ │ │ │ │ │ │ └── images │ │ │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ │ └── style.css │ │ │ │ │ │ └── single_graph.html │ │ │ │ └── not_pairs_containment_distance.tsv │ │ │ │ ├── dcj_thresh_4_graph │ │ │ │ ├── .snakemake_timestamp │ │ │ │ ├── objects │ │ │ │ │ ├── communities.pkl │ │ │ │ │ ├── hub_plasmids.csv │ │ │ │ │ ├── subcommunities.pkl │ │ │ │ │ └── typing.tsv │ │ │ │ └── visualisations │ │ │ │ │ ├── communities │ │ │ │ │ ├── graphs │ │ │ │ │ │ └── community_0.html │ │ │ │ │ ├── index.html │ │ │ │ │ └── libs │ │ │ │ │ │ ├── bluebird.js │ │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ │ ├── resources │ │ │ │ │ │ └── images │ │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ │ └── style.css │ │ │ │ │ └── subcommunities │ │ │ │ │ ├── graphs │ │ │ │ │ └── community_0_subcommunity_0.html │ │ │ │ │ ├── index.html │ │ │ │ │ └── libs │ │ │ │ │ ├── bluebird.js │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ ├── resources │ │ │ │ │ └── images │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ └── style.css │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ ├── batch_0_map.txt │ │ │ │ ├── batch_10_align.unimog │ │ │ │ ├── batch_10_map.txt │ │ │ │ ├── batch_1_align.unimog │ │ │ │ ├── batch_1_map.txt │ │ │ │ ├── batch_2_align.unimog │ │ │ │ ├── batch_2_map.txt │ │ │ │ ├── batch_3_align.unimog │ │ │ │ ├── batch_3_map.txt │ │ │ │ ├── batch_4_align.unimog │ │ │ │ ├── batch_4_map.txt │ │ │ │ ├── batch_5_align.unimog │ │ │ │ ├── batch_5_map.txt │ │ │ │ ├── batch_6_align.unimog │ │ │ │ ├── batch_6_map.txt │ │ │ │ ├── batch_7_align.unimog │ │ │ │ ├── batch_7_map.txt │ │ │ │ ├── batch_8_align.unimog │ │ │ │ ├── batch_8_map.txt │ │ │ │ ├── batch_9_align.unimog │ │ │ │ └── batch_9_map.txt │ │ ├── input │ │ │ ├── fastas │ │ │ │ ├── genome_1.fna │ │ │ │ ├── genome_4.fna │ │ │ │ └── genome_8.fna │ │ │ └── palindrome.txt │ │ └── palindrome │ │ │ └── truth │ │ │ └── align │ │ │ ├── all_plasmids_distances.tsv │ │ │ ├── batches │ │ │ ├── .snakemake_timestamp │ │ │ ├── batch_0.txt │ │ │ └── batching_info.txt │ │ │ ├── containment │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ └── containment_communities │ │ │ │ ├── .snakemake_timestamp │ │ │ │ ├── objects │ │ │ │ ├── communities.pkl │ │ │ │ ├── communities.tsv │ │ │ │ ├── communities.txt │ │ │ │ └── plasmid_graph.pkl │ │ │ │ └── visualisations │ │ │ │ ├── communities │ │ │ │ ├── graphs │ │ │ │ │ └── community_0.html │ │ │ │ ├── index.html │ │ │ │ └── libs │ │ │ │ │ ├── bluebird.js │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ ├── resources │ │ │ │ │ └── images │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ └── style.css │ │ │ │ └── single_graph │ │ │ │ ├── libs │ │ │ │ ├── bluebird.js │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ ├── cytoscape-euler.js │ │ │ │ ├── cytoscape-layers.js │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ ├── cytoscape.min.js │ │ │ │ ├── fetch.min.js │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ ├── jquery-ui.min.css │ │ │ │ ├── jquery-ui.min.js │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ ├── jquery.blockUI.js │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ ├── resources │ │ │ │ │ └── images │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ └── style.css │ │ │ │ └── single_graph.html │ │ │ ├── dcj_thresh_4_graph │ │ │ ├── .snakemake_timestamp │ │ │ ├── objects │ │ │ │ ├── communities.pkl │ │ │ │ ├── hub_plasmids.csv │ │ │ │ ├── subcommunities.pkl │ │ │ │ └── typing.tsv │ │ │ └── visualisations │ │ │ │ ├── communities │ │ │ │ ├── graphs │ │ │ │ │ └── community_0.html │ │ │ │ ├── index.html │ │ │ │ └── libs │ │ │ │ │ ├── bluebird.js │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ ├── resources │ │ │ │ │ └── images │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ └── style.css │ │ │ │ └── subcommunities │ │ │ │ ├── graphs │ │ │ │ └── community_0_subcommunity_0.html │ │ │ │ ├── index.html │ │ │ │ └── libs │ │ │ │ ├── bluebird.js │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ ├── cytoscape-euler.js │ │ │ │ ├── cytoscape-layers.js │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ ├── cytoscape.min.js │ │ │ │ ├── fetch.min.js │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ ├── jquery-ui.min.css │ │ │ │ ├── jquery-ui.min.js │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ ├── jquery.blockUI.js │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ ├── resources │ │ │ │ └── images │ │ │ │ │ ├── busy.gif │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ └── style.css │ │ │ └── unimogs │ │ │ ├── batch_0_align.unimog │ │ │ └── batch_0_map.txt │ ├── indel_tests │ │ ├── input │ │ │ ├── fastas │ │ │ │ ├── CP055413.1.fna │ │ │ │ ├── CP056587.1.fna │ │ │ │ ├── LR890289.1.fna │ │ │ │ ├── LR890465.1.fna │ │ │ │ ├── NC_006816.1.fna │ │ │ │ ├── NZ_CP006799.1.fna │ │ │ │ ├── NZ_CP013657.1.fna │ │ │ │ ├── NZ_CP019161.1.fna │ │ │ │ ├── NZ_CP037912.1.fna │ │ │ │ ├── NZ_CP042975.1.fna │ │ │ │ ├── NZ_CP047745.1.fna │ │ │ │ ├── NZ_CP051708.1.fna │ │ │ │ ├── NZ_CP054769.1.fna │ │ │ │ ├── NZ_CP069936.1.fna │ │ │ │ ├── NZ_CP070577.1.fna │ │ │ │ ├── NZ_CP072977.1.fna │ │ │ │ ├── NZ_CP075435.1.fna │ │ │ │ ├── NZ_CP102837.1.fna │ │ │ │ ├── NZ_CP129874.1.fna │ │ │ │ ├── NZ_MH477636.1.fna │ │ │ │ ├── NZ_MK312248.1.fna │ │ │ │ ├── NZ_MT035874.1.fna │ │ │ │ └── NZ_MW245019.1.fna │ │ │ ├── test_1.txt │ │ │ ├── test_10.txt │ │ │ ├── test_11.txt │ │ │ ├── test_2.txt │ │ │ ├── test_3.txt │ │ │ ├── test_4.txt │ │ │ ├── test_5.txt │ │ │ ├── test_6.txt │ │ │ ├── test_7.txt │ │ │ ├── test_8.txt │ │ │ └── test_9.txt │ │ ├── test_1 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_10 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_11 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_2 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_3 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_4 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_5 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_6 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_7 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ ├── test_8 │ │ │ └── truth │ │ │ │ └── align │ │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ └── batch_0_map.txt │ │ └── test_9 │ │ │ └── truth │ │ │ └── align │ │ │ ├── containment │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ └── containment_communities │ │ │ │ └── objects │ │ │ │ ├── communities.tsv │ │ │ │ └── communities.txt │ │ │ └── unimogs │ │ │ ├── batch_0_align.unimog │ │ │ └── batch_0_map.txt │ └── toy_tests │ │ ├── input │ │ ├── fastas │ │ │ ├── 2_dup_3_dup.fna │ │ │ ├── 3_dup.fna │ │ │ ├── 3_dup_w_inverse.fna │ │ │ ├── del_rearrange.fna │ │ │ ├── dup_and_inverse.fna │ │ │ ├── inverse_block.fna │ │ │ ├── inversion.fna │ │ │ ├── outlier.fna │ │ │ ├── reference.fna │ │ │ ├── reference_2.fna │ │ │ └── reverse.fna │ │ ├── skip.unimog │ │ ├── test_1.txt │ │ └── test_2.txt │ │ ├── test_1 │ │ └── truth │ │ │ ├── align │ │ │ ├── all_plasmids_distances.tsv │ │ │ ├── batches │ │ │ │ ├── batch_0.txt │ │ │ │ ├── batch_1.txt │ │ │ │ ├── batch_2.txt │ │ │ │ └── batching_info.txt │ │ │ ├── containment │ │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ │ └── containment_communities │ │ │ │ │ └── objects │ │ │ │ │ ├── communities.tsv │ │ │ │ │ └── communities.txt │ │ │ ├── dcj_thresh_4_graph │ │ │ │ └── objects │ │ │ │ │ ├── hub_plasmids.csv │ │ │ │ │ └── typing.tsv │ │ │ └── unimogs │ │ │ │ ├── batch_0_align.unimog │ │ │ │ ├── batch_0_map.txt │ │ │ │ ├── batch_1_align.unimog │ │ │ │ ├── batch_1_map.txt │ │ │ │ ├── batch_2_align.unimog │ │ │ │ └── batch_2_map.txt │ │ │ └── skip │ │ │ ├── all_plasmids_distances.tsv │ │ │ ├── batches │ │ │ ├── .snakemake_timestamp │ │ │ ├── batch_0.txt │ │ │ ├── batch_1.txt │ │ │ ├── batch_2.txt │ │ │ └── batching_info.txt │ │ │ ├── containment │ │ │ ├── all_pairs_containment_distance.tsv │ │ │ └── containment_communities │ │ │ │ ├── .snakemake_timestamp │ │ │ │ ├── objects │ │ │ │ ├── communities.pkl │ │ │ │ ├── communities.tsv │ │ │ │ ├── communities.txt │ │ │ │ └── plasmid_graph.pkl │ │ │ │ └── visualisations │ │ │ │ ├── communities │ │ │ │ ├── graphs │ │ │ │ │ ├── community_0.html │ │ │ │ │ └── community_1.html │ │ │ │ ├── index.html │ │ │ │ └── libs │ │ │ │ │ ├── bluebird.js │ │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ │ ├── cytoscape-euler.js │ │ │ │ │ ├── cytoscape-layers.js │ │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ │ ├── cytoscape.min.js │ │ │ │ │ ├── fetch.min.js │ │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ │ ├── jquery-ui.min.css │ │ │ │ │ ├── jquery-ui.min.js │ │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ │ ├── jquery.blockUI.js │ │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ │ ├── resources │ │ │ │ │ └── images │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ │ └── style.css │ │ │ │ └── single_graph │ │ │ │ ├── libs │ │ │ │ ├── bluebird.js │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ ├── cytoscape-euler.js │ │ │ │ ├── cytoscape-layers.js │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ ├── cytoscape.min.js │ │ │ │ ├── fetch.min.js │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ ├── jquery-ui.min.css │ │ │ │ ├── jquery-ui.min.js │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ ├── jquery.blockUI.js │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ ├── resources │ │ │ │ │ └── images │ │ │ │ │ │ ├── busy.gif │ │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ └── style.css │ │ │ │ └── single_graph.html │ │ │ └── dcj_thresh_4_graph │ │ │ ├── .snakemake_timestamp │ │ │ ├── objects │ │ │ ├── communities.pkl │ │ │ ├── hub_plasmids.csv │ │ │ ├── subcommunities.pkl │ │ │ └── typing.tsv │ │ │ └── visualisations │ │ │ ├── communities │ │ │ ├── graphs │ │ │ │ ├── community_0.html │ │ │ │ └── community_1.html │ │ │ ├── index.html │ │ │ └── libs │ │ │ │ ├── bluebird.js │ │ │ │ ├── cytoscape-bubblesets.js │ │ │ │ ├── cytoscape-euler.js │ │ │ │ ├── cytoscape-layers.js │ │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ │ ├── cytoscape.min.js │ │ │ │ ├── fetch.min.js │ │ │ │ ├── jquery-3.6.0.min.js │ │ │ │ ├── jquery-ui.min.css │ │ │ │ ├── jquery-ui.min.js │ │ │ │ ├── jquery-ui.structure.min.css │ │ │ │ ├── jquery-ui.theme.min.css │ │ │ │ ├── jquery.blockUI.js │ │ │ │ ├── jquery.layout-1.4.0.js │ │ │ │ ├── resources │ │ │ │ └── images │ │ │ │ │ ├── busy.gif │ │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ │ └── style.css │ │ │ └── subcommunities │ │ │ ├── graphs │ │ │ ├── community_0_subcommunity_0.html │ │ │ └── community_1_subcommunity_0.html │ │ │ ├── index.html │ │ │ └── libs │ │ │ ├── bluebird.js │ │ │ ├── cytoscape-bubblesets.js │ │ │ ├── cytoscape-euler.js │ │ │ ├── cytoscape-layers.js │ │ │ ├── cytoscape-ngraph.forcelayout.js │ │ │ ├── cytoscape.min.js │ │ │ ├── fetch.min.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.min.css │ │ │ ├── jquery.blockUI.js │ │ │ ├── jquery.layout-1.4.0.js │ │ │ ├── resources │ │ │ └── images │ │ │ │ ├── busy.gif │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ └── style.css │ │ └── test_2 │ │ └── truth │ │ └── align │ │ ├── all_plasmids_distances.tsv │ │ ├── batches │ │ ├── .snakemake_timestamp │ │ ├── batch_0.txt │ │ ├── batch_1.txt │ │ ├── batch_10.txt │ │ ├── batch_2.txt │ │ ├── batch_3.txt │ │ ├── batch_4.txt │ │ ├── batch_5.txt │ │ ├── batch_6.txt │ │ ├── batch_7.txt │ │ ├── batch_8.txt │ │ ├── batch_9.txt │ │ └── batching_info.txt │ │ ├── containment │ │ ├── all_pairs_containment_distance.tsv │ │ └── containment_communities │ │ │ └── objects │ │ │ ├── communities.tsv │ │ │ └── communities.txt │ │ ├── dcj_thresh_4_graph │ │ └── objects │ │ │ ├── hub_plasmids.csv │ │ │ └── typing.tsv │ │ └── unimogs │ │ ├── batch_0_align.unimog │ │ ├── batch_0_map.txt │ │ ├── batch_10_align.unimog │ │ ├── batch_10_map.txt │ │ ├── batch_1_align.unimog │ │ ├── batch_1_map.txt │ │ ├── batch_2_align.unimog │ │ ├── batch_2_map.txt │ │ ├── batch_3_align.unimog │ │ ├── batch_3_map.txt │ │ ├── batch_4_align.unimog │ │ ├── batch_4_map.txt │ │ ├── batch_5_align.unimog │ │ ├── batch_5_map.txt │ │ ├── batch_6_align.unimog │ │ ├── batch_6_map.txt │ │ ├── batch_7_align.unimog │ │ ├── batch_7_map.txt │ │ ├── batch_8_align.unimog │ │ ├── batch_8_map.txt │ │ ├── batch_9_align.unimog │ │ └── batch_9_map.txt └── test_unimog_tests.py └── utils.py /.github/workflows/ci.yaml: -------------------------------------------------------------------------------- 1 | name: Test pling 2 | 3 | on: 4 | push: 5 | branches: 6 | - main 7 | - dev 8 | pull_request: 9 | branches: 10 | - main 11 | - dev 12 | 13 | jobs: 14 | Testing: 15 | runs-on: ${{ matrix.os }} 16 | strategy: 17 | matrix: 18 | os: [ ubuntu-latest ] 19 | python-version: [ 3.9, "3.10", 3.11 ] 20 | steps: 21 | - uses: actions/checkout@v3 22 | - uses: mamba-org/setup-micromamba@v1 23 | with: 24 | micromamba-version: '1.5.8-0' 25 | environment-name: test-env 26 | condarc: | 27 | channels: 28 | - conda-forge 29 | - bioconda 30 | - defaults 31 | create-args: >- 32 | python=${{ matrix.python-version }} 33 | sourmash 34 | pandas 35 | numpy 36 | intervaltree 37 | mummer=3.23 38 | glpk=5.0 39 | snakemake=7.32.4 40 | plasnet=0.6.0 41 | dingII 42 | init-shell: bash 43 | cache-environment: true 44 | post-cleanup: 'all' 45 | 46 | - uses: eWaterCycle/setup-singularity@v7 47 | with: 48 | singularity-version: 3.7.1 49 | 50 | - name: Test 51 | shell: bash -el {0} 52 | run: | 53 | micromamba activate test-env 54 | python -m pip install . 55 | PYTHONPATH="." python -m unittest discover -s tests -t . 56 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .idea 2 | .snakemake 3 | __pycache__ 4 | logs 5 | /.venv/ 6 | -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yaml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | # Required 6 | version: 2 7 | 8 | # Set the OS, Python version and other tools you might need 9 | build: 10 | os: ubuntu-22.04 11 | tools: 12 | python: "3.12" 13 | # You can also specify other tool versions: 14 | # nodejs: "19" 15 | # rust: "1.64" 16 | # golang: "1.19" 17 | 18 | # Build documentation in the "docs/" directory with Sphinx 19 | sphinx: 20 | configuration: docs/conf.py 21 | 22 | # Optionally build your docs in additional formats such as PDF and ePub 23 | # formats: 24 | # - pdf 25 | # - epub 26 | 27 | # Optional but recommended, declare the Python requirements required 28 | # to build your documentation 29 | # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html 30 | python: 31 | install: 32 | - requirements: docs/requirements.txt 33 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2023 iqbal-lab-org 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include pling/resources.tsv 2 | include pling/align_snakemake/Snakefile 3 | include pling/batching/Snakefile 4 | include pling/dcj_snakemake/Snakefile 5 | include pling/common_rules/common_rules.smk 6 | include pling/jac_network_snakemake/Snakefile 7 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Pling! 2 | 3 | Pling is a software workflow for plasmid analysis using rearrangement distances, specifically the Double Cut and Join Indel (DCJ-Indel) distance. By intelligently combining containment distance (shared content as fraction of the smaller) and DCJ-indel distance ("how far apart evolutionarily" in a structural sense), and by preventing shared mobile elements from clouding the issue, it infers clusters of related plasmids. 4 | 5 | For installation instructions and documentation, please go [here](https://pling.readthedocs.io). 6 | -------------------------------------------------------------------------------- /docs/basic.rst: -------------------------------------------------------------------------------- 1 | Basic Usage 2 | =========== 3 | 4 | Required input is a text file of a list of paths to fasta files ``genomes_list`` and a path to an output directory ``output_dir``. All the genomes must be circular and complete. If you have all your genomes in one directory, you can navigate to that directory and generate ``genomes_list`` by running 5 | 6 | .. code-block:: console 7 | 8 | ls -d -1 $PWD/*.fasta > input.txt 9 | 10 | Then usage is 11 | 12 | .. code-block:: console 13 | 14 | pling input.txt output_dir align 15 | 16 | 17 | -------------------------------------------------------------------------------- /docs/citation.rst: -------------------------------------------------------------------------------- 1 | Citation 2 | ======== 3 | 4 | Preprint: https://doi.org/10.1101/2024.06.12.598623 5 | -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # This file only contains a selection of the most common options. For a full 4 | # list see the documentation: 5 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 6 | 7 | # -- Path setup -------------------------------------------------------------- 8 | 9 | # If extensions (or modules to document with autodoc) are in another directory, 10 | # add these directories to sys.path here. If the directory is relative to the 11 | # documentation root, use os.path.abspath to make it absolute, like shown here. 12 | # 13 | # import os 14 | # import sys 15 | # sys.path.insert(0, os.path.abspath('.')) 16 | 17 | 18 | # -- Project information ----------------------------------------------------- 19 | 20 | project = "pling" 21 | copyright = "2024, Daria Frolova" 22 | author = "Daria Frolova" 23 | 24 | release = '2.0' 25 | version = '2.0.0' 26 | 27 | # -- General configuration --------------------------------------------------- 28 | # -- General configuration 29 | 30 | extensions = [ 31 | "sphinx.ext.duration", 32 | "sphinx.ext.doctest", 33 | "sphinx.ext.autodoc", 34 | "sphinx.ext.autosummary", 35 | "sphinx.ext.intersphinx", 36 | ] 37 | 38 | intersphinx_mapping = { 39 | "rtd": ("https://docs.readthedocs.io/en/stable/", None), 40 | "python": ("https://docs.python.org/3/", None), 41 | "sphinx": ("https://www.sphinx-doc.org/en/master/", None), 42 | } 43 | intersphinx_disabled_domains = ["std"] 44 | 45 | templates_path = ["_templates"] 46 | 47 | # -- Options for EPUB output 48 | epub_show_urls = "footnote" 49 | 50 | # List of patterns, relative to source directory, that match files and 51 | # directories to ignore when looking for source files. 52 | # This pattern also affects html_static_path and html_extra_path. 53 | exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] 54 | 55 | # -- Options for HTML output ------------------------------------------------- 56 | 57 | # The theme to use for HTML and HTML Help pages. See the documentation for 58 | # a list of builtin themes. 59 | # 60 | html_theme = "sphinx_book_theme" 61 | # Add any paths that contain custom static files (such as style sheets) here, 62 | # relative to this directory. They are copied after the builtin static files, 63 | # so a file named "default.css" will overwrite the builtin "default.css". 64 | html_static_path = ["_static"] 65 | -------------------------------------------------------------------------------- /docs/images/com_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/com_0.png -------------------------------------------------------------------------------- /docs/images/com_0_155.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/com_0_155.png -------------------------------------------------------------------------------- /docs/images/com_index.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/com_index.png -------------------------------------------------------------------------------- /docs/images/example_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/example_1.png -------------------------------------------------------------------------------- /docs/images/plasmid_cointegrates.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/plasmid_cointegrates.png -------------------------------------------------------------------------------- /docs/images/russian_dolls_fusion.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/russian_dolls_fusion.png -------------------------------------------------------------------------------- /docs/images/russian_dolls_network.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/docs/images/russian_dolls_network.png -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | Pling! 2 | ====== 3 | 4 | Pling is a software workflow for plasmid analysis using rearrangement distances, specifically the Double Cut and Join Indel (DCJ-Indel) distance. By intelligently combining containment distance (shared content as fraction of the smaller) and DCJ-indel distance ("how far apart evolutionarily" in a structural sense), and by preventing shared mobile elements from clouding the issue, it infers clusters of related plasmids. 5 | 6 | .. toctree:: 7 | 8 | installation.rst 9 | basic.rst 10 | tutorial.rst 11 | output.rst 12 | advanced.rst 13 | tips.rst 14 | citation.rst 15 | -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- 1 | Installation 2 | ============ 3 | 4 | Conda 5 | ----- 6 | 7 | To install with conda, just run:: 8 | 9 | conda config --add channels bioconda 10 | conda config --add channels conda-forge 11 | conda install pling 12 | 13 | 14 | From source 15 | ----------- 16 | 17 | Start with:: 18 | 19 | git clone https://github.com/iqbal-lab-org/pling.git && cd pling 20 | 21 | From here you can install dependancies using conda with the ``env.yaml`` file, or whichever method you prefer. To install dependancies with conda, do:: 22 | 23 | conda env create -f env.yaml 24 | conda activate pling 25 | 26 | and then finally install pling with:: 27 | 28 | python -m pip install . 29 | 30 | 31 | Installing optional dependancies 32 | -------------------------------- 33 | 34 | By default, the DCJ-Indel distances are calculated with the open source solver GLPK. Optionally, pling can use Gurobi for its calculations, but this dependancy is not included in the usual pling installation. This is because Gurobi is a commercial software which requires a license, which is free for academic purposes. Information on obtaining this license can be found here: https://www.gurobi.com/academia/academic-program-and-licenses/. Gurobi can then be installed via conda as follows:: 35 | 36 | conda config --add channels https://conda.anaconda.org/gurobi 37 | conda install gurobi=10.0.1 38 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | sphinx==7.1.2 2 | sphinx-book-theme 3 | -------------------------------------------------------------------------------- /env.yaml: -------------------------------------------------------------------------------- 1 | name: pling 2 | channels: 3 | - conda-forge 4 | - bioconda 5 | dependencies: 6 | - python =3.10 7 | - snakemake =7.32.4 8 | - sourmash =4.4.0 9 | - pandas =1.5.3 10 | - numpy =1.26.0 11 | - intervaltree =3.0.2 12 | - mummer =3.23 13 | - glpk =5.0 14 | - plasnet==0.6.0 15 | - dingII 16 | -------------------------------------------------------------------------------- /pling/__init__.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | """ 4 | Version has unique source in pyproject.toml. 5 | importlib fetches version from distribution metadata files 6 | (in dist-info or egg-info dirs). 7 | From Python 3.8, importlib_metadata is in standard library as importlib.metadata. 8 | """ 9 | if sys.version_info >= (3, 8): 10 | from importlib import metadata 11 | else: 12 | import importlib_metadata as metadata 13 | 14 | __version__: str = metadata.version("pling") 15 | 16 | from .run_pling import main 17 | 18 | __all__ = ["main"] 19 | -------------------------------------------------------------------------------- /pling/align_snakemake/Snakefile: -------------------------------------------------------------------------------- 1 | import os 2 | import pandas as pd 3 | import math 4 | from pling.utils import get_pling_root_dir, get_fasta_file_info 5 | 6 | configfile: "../config.yaml" 7 | 8 | OUTPUTPATH = config["output_dir"] 9 | PREFIX = config["prefix"] 10 | batch_size = config["batch_size"] 11 | FASTAFILES = [el[0] for el in pd.read_csv(config["genomes_list"], header=None).values] 12 | FASTAEXT = {os.path.splitext(os.path.basename(el))[0]:os.path.splitext(os.path.basename(el))[1] for el in FASTAFILES} 13 | GENOMES = list(FASTAEXT.keys()) 14 | 15 | def get_regions(): 16 | if config.get("regions", False): 17 | return "--regions" 18 | else: 19 | return "" 20 | 21 | def get_topology(topology): 22 | if config["topology"]=="None": 23 | return "" 24 | else: 25 | return f"--topology {topology}" 26 | 27 | include: "../common_rules/common_rules.smk" 28 | 29 | rule all: 30 | input: 31 | seq_containment = f"{OUTPUTPATH}/containment/all_pairs_containment_distance.tsv", 32 | communities = f"{OUTPUTPATH}/containment/containment_communities" 33 | 34 | rule make_unimogs: 35 | input: 36 | batch_list=lambda wildcards: f"{OUTPUTPATH}/batches/batch_{wildcards.batch}.txt" 37 | output: 38 | containment=f"{OUTPUTPATH}/tmp_files/containment_batchwise/batch_{{batch}}_containment.tsv", 39 | unimog = f"{OUTPUTPATH}/unimogs/batch_{{batch}}_align.unimog", 40 | map = f"{OUTPUTPATH}/unimogs/batch_{{batch}}_map.txt" 41 | threads: config["make_unimogs_threads"] 42 | resources: 43 | mem_mb=lambda wildcards, attempt: config["make_unimogs_mem"]*attempt 44 | params: 45 | genomes_list = config["genomes_list"], 46 | outputpath = OUTPUTPATH, 47 | identity_threshold = config["identity_threshold"], 48 | containment_distance = config["seq_containment_distance"], 49 | pling_root_dir = get_pling_root_dir(), 50 | regions = get_regions(), 51 | topology = get_topology(config["topology"]) 52 | shadow: "shallow" 53 | shell: 54 | """ 55 | PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/align_snakemake/unimog.py \ 56 | --genomes_list {params.genomes_list} \ 57 | --batch {input.batch_list} \ 58 | --identity_threshold {params.identity_threshold} \ 59 | --containment_distance {params.containment_distance} \ 60 | --outputpath {params.outputpath} \ 61 | --containment_output {output.containment} \ 62 | --unimog_output {output.unimog} \ 63 | --map_output {output.map} \ 64 | {params.regions} \ 65 | {params.topology} 66 | """ 67 | -------------------------------------------------------------------------------- /pling/batching/Snakefile: -------------------------------------------------------------------------------- 1 | from pling.utils import get_pling_root_dir 2 | 3 | OUTPUTPATH = config["output_dir"] 4 | 5 | def smash(): 6 | if config.get("sourmash", False): 7 | return "--sourmash" 8 | else: 9 | return "" 10 | 11 | def get_batching_resources(type): 12 | if config.get("sourmash", False): 13 | threads = config["sourmash_threads"] 14 | mem = config["sourmash_mem"] 15 | else: 16 | threads = 1 17 | mem = 4000 18 | if type == "threads": 19 | return threads 20 | elif type == "mem": 21 | return mem 22 | 23 | rule all: 24 | input: 25 | f"{OUTPUTPATH}/batches" 26 | 27 | rule get_batches: 28 | output: 29 | directory(f"{OUTPUTPATH}/batches") 30 | params: 31 | outputpath = OUTPUTPATH, 32 | genomes_list = config["genomes_list"], 33 | batch_size = config["batch_size"], 34 | sourmash = smash(), 35 | smash_threshold = config.get("sourmash_threshold", 1), 36 | containmentpath = f"{OUTPUTPATH}/containment/not_pairs_containment_distance.tsv", 37 | pling_root_dir = get_pling_root_dir() 38 | threads: get_batching_resources("threads") 39 | resources: 40 | mem_mb=lambda wildcards, attempt: get_batching_resources("mem")*attempt 41 | shell: 42 | """ 43 | PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/batching/get_batches.py \ 44 | --genomes_list {params.genomes_list} \ 45 | --batch_size {params.batch_size} \ 46 | --outputpath {params.outputpath} \ 47 | {params.sourmash} \ 48 | --smash_threshold {params.smash_threshold} \ 49 | --containmentpath {params.containmentpath} 50 | """ 51 | -------------------------------------------------------------------------------- /pling/common_rules/common_rules.smk: -------------------------------------------------------------------------------- 1 | # common rules and functions shared by align_snakemake and jac_network_snakemake workflows 2 | # TODO: refactor as this is a bit brittle because it requires the predefinition of the following global variables 3 | # TODO: prior to including this: 4 | # OUTPUTPATH 5 | # GENOMES 6 | from pling.utils import get_number_of_batches 7 | 8 | rule create_genomes_tsv: 9 | output: 10 | genomes_tsv = f"{OUTPUTPATH}/tmp_files/genomes.tsv" 11 | params: 12 | genomes = GENOMES 13 | run: 14 | with open(output.genomes_tsv, "w") as f: 15 | f.write("plasmid\n") 16 | for genome in params.genomes: 17 | f.write(f"{genome}\n") 18 | localrules: create_genomes_tsv 19 | 20 | rule cat_containment: 21 | input: 22 | containments = expand(f"{OUTPUTPATH}/tmp_files/containment_batchwise/batch_{{batch}}_containment.tsv", batch=[str(i) for i in range(get_number_of_batches(OUTPUTPATH))]) 23 | output: 24 | all_containment_distances = f"{OUTPUTPATH}/containment/all_pairs_containment_distance.tsv" 25 | threads: 1 26 | resources: 27 | mem_mb=lambda wildcards, attempt: 4000*attempt 28 | run: 29 | with open(output.all_containment_distances, "w") as contain_out: 30 | contain_out.write("plasmid_1\tplasmid_2\tdistance\n") 31 | for file in input.containments: 32 | with open(file, "r") as f: 33 | to_cat = f.read() 34 | contain_out.write(to_cat) 35 | 36 | localrules: cat_containment 37 | 38 | def get_metadata(metadata): 39 | if metadata == "None": 40 | return "" 41 | else: 42 | return f"--plasmids-metadata {metadata}" 43 | 44 | rule get_communities: 45 | input: 46 | containment = f"{OUTPUTPATH}/containment/all_pairs_containment_distance.tsv", 47 | genomes = rules.create_genomes_tsv.output.genomes_tsv 48 | output: 49 | communities = directory(f"{OUTPUTPATH}/containment/containment_communities"), 50 | threads: 1 51 | resources: 52 | mem_mb=lambda wildcards, attempt: config["get_communities_mem"]*attempt 53 | params: 54 | containment_distance=config["seq_containment_distance"], 55 | bh_connectivity=config["bh_connectivity"], 56 | bh_neighbours_edge_density=config["bh_neighbours_edge_density"], 57 | metadata = get_metadata(config["metadata"]), 58 | output_type = config["output_type"] 59 | shell: """ 60 | plasnet split \ 61 | --distance-threshold {params.containment_distance} \ 62 | --bh-connectivity {params.bh_connectivity} \ 63 | --bh-neighbours-edge-density {params.bh_neighbours_edge_density} \ 64 | --output-plasmid-graph \ 65 | --output-type {params.output_type} \ 66 | {params.metadata} \ 67 | {input.genomes} \ 68 | {input.containment} \ 69 | {output.communities} 70 | """ 71 | -------------------------------------------------------------------------------- /pling/dcj_snakemake/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/pling/dcj_snakemake/__init__.py -------------------------------------------------------------------------------- /pling/dcj_snakemake/glpk_and_ding.py: -------------------------------------------------------------------------------- 1 | import subprocess 2 | 3 | def unimog_to_ilp(unimog, lp, genome1, genome2): 4 | try: 5 | print("Converting unimog to ILP...\n") 6 | subprocess.run(f"dingII generate {unimog} -mm --writeilp {lp} -p {genome1} {genome2}", shell=True, check=True, capture_output=True) 7 | print("Completed.\n") 8 | except subprocess.CalledProcessError as e: 9 | print(e.stderr.decode()) 10 | print(e) 11 | raise e 12 | 13 | def ilp_GLPK(lp, solution, snakefile_dir, timelimit): 14 | try: 15 | print("Solving ILP with GLPK...\n") 16 | subprocess.run(f"glpsol --lp {lp} -o {solution}.tmp {timelimit}", shell=True, check=True, capture_output=True) 17 | print("Completed.\n Converting GLPK output to Gurobi output...\n") 18 | subprocess.run(f"python {snakefile_dir}/glpk_sol_to_gurobi_sol.py <{solution}.tmp >{solution}", shell=True, check=True, capture_output=True) 19 | print("Completed.\n") 20 | subprocess.run(f"rm {solution}.tmp", shell=True, check=True, capture_output=True) 21 | except subprocess.CalledProcessError as e: 22 | print(e.stderr.decode()) 23 | print(e) 24 | raise e 25 | 26 | def dcj_dist(unimog, solution, genome1, genome2): 27 | try: 28 | print("Parsing Gurobi output to get DCJ distances...\n") 29 | dcj_out = subprocess.run(f"dingII parsesol {unimog} --solgur {solution} -p {genome1} {genome2}", shell=True, check=True, capture_output=True, text=True).stdout 30 | dist = int(dcj_out.strip().split(" ")[2]) 31 | print("Completed.\n") 32 | except subprocess.CalledProcessError as e: 33 | print(e.stderr.decode()) 34 | print(e) 35 | raise e 36 | return dist 37 | -------------------------------------------------------------------------------- /pling/dcj_snakemake/glpk_sol_to_gurobi_sol.py: -------------------------------------------------------------------------------- 1 | def glpk_sol_to_gurobi_sol(input_fh, output_fh): 2 | print("# Solution for model obj", file=output_fh) 3 | 4 | gather_solution = False 5 | solution = [] 6 | for line in input_fh: 7 | line = line.strip() 8 | 9 | is_objective_line = line.startswith("Objective:") 10 | if is_objective_line: 11 | obj_value = int(line.split()[3]) 12 | print(f"# Objective value = {obj_value}", file=output_fh) 13 | 14 | solution_started = line == "No. Column name Activity Lower bound Upper bound" 15 | if solution_started: 16 | gather_solution = True 17 | 18 | solution_ended = line.startswith("Integer feasibility conditions:") 19 | if solution_ended: 20 | gather_solution = False 21 | 22 | if gather_solution: 23 | solution.extend(line.split()) 24 | 25 | headerless_solution = solution[13:] 26 | for number, column_name, star, activity, lower_bound, upper_bound in zip(*(iter(headerless_solution[i::6]) for i in range(0, 6))): 27 | print(column_name, activity, file=output_fh) 28 | 29 | 30 | if __name__ == "__main__": 31 | import sys 32 | sys.exit(glpk_sol_to_gurobi_sol(sys.stdin, sys.stdout)) 33 | -------------------------------------------------------------------------------- /pling/jac_network_snakemake/Snakefile: -------------------------------------------------------------------------------- 1 | import os 2 | import pandas as pd 3 | from pling.utils import get_pling_root_dir 4 | import math 5 | 6 | configfile: "../config.yaml" 7 | 8 | FASTAFILES = [el[0] for el in pd.read_csv(config["genomes_list"], header=None).values] 9 | FASTAEXT = {os.path.splitext(os.path.basename(el))[0]:os.path.splitext(os.path.basename(el))[1] for el in FASTAFILES} 10 | GENOMES = list(FASTAEXT.keys()) 11 | FASTAPATH = os.path.dirname(FASTAFILES[0]) 12 | OUTPUTPATH = config["output_dir"] 13 | PREFIX = config["prefix"] 14 | batch_size = config["batch_size"] 15 | number_of_batches = math.ceil((len(GENOMES)*(len(GENOMES)-1)/2)/batch_size) 16 | 17 | include: "../common_rules/common_rules.smk" 18 | 19 | rule all: 20 | input: 21 | communities = f"{OUTPUTPATH}/containment/containment_communities" 22 | 23 | rule pairwise_seq_containment: 24 | input: 25 | batch_list=lambda wildcards: f"{OUTPUTPATH}/batches/batch_{wildcards.batch}.txt" 26 | output: 27 | containment=f"{OUTPUTPATH}/tmp_files/containment_batchwise/batch_{{batch}}_containment.tsv" 28 | threads: config["pairwise_seq_containment_threads"] 29 | resources: 30 | mem_mb=lambda wildcards, attempt: config["pairwise_seq_containment_mem"]*attempt 31 | params: 32 | genomes_list = config["genomes_list"], 33 | batch = lambda wildcards: wildcards.batch, 34 | outputpath = OUTPUTPATH, 35 | identity_threshold = config["identity_threshold"], 36 | pling_root_dir = get_pling_root_dir() 37 | shadow: "shallow" 38 | shell: """ 39 | PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/jac_network_snakemake/seq_containment.py \ 40 | --genomes_list {params.genomes_list} \ 41 | --batch {params.batch} \ 42 | --identity_threshold {params.identity_threshold} \ 43 | --outputpath {params.outputpath} \ 44 | --containment_output {output.containment} \ 45 | """ 46 | -------------------------------------------------------------------------------- /pling/resources.tsv: -------------------------------------------------------------------------------- 1 | Rule Threads Mem 2 | make_unimogs 1 10000 3 | get_communities NA 4000 4 | bakta 1 15000 5 | panaroo 1 15000 6 | minimap 1 4000 7 | consolidation NA 4000 8 | deduplication 1 10000 9 | blocks NA 4000 10 | unimog_to_ilp NA 4000 11 | ilp 1 10000 12 | dcj_dist NA 4000 13 | dcj_matrix NA 4000 14 | build_DCJ_graph NA 8000 15 | pairwise_seq_containment 1 10000 16 | sourmash 1 10000 17 | -------------------------------------------------------------------------------- /pling/utils.py: -------------------------------------------------------------------------------- 1 | from pathlib import Path 2 | import os 3 | import pandas as pd 4 | 5 | def get_pling_root_dir() -> Path: 6 | return Path(__file__).parent.parent 7 | 8 | def get_number_of_batches(outputpath): 9 | with open(f"{outputpath}/batches/batching_info.txt") as f: 10 | batch_size, number_of_batches = f.readlines() 11 | return int(number_of_batches) 12 | 13 | def read_in_batch_pairs(filepath): 14 | pairs=[] 15 | with open(filepath,"r") as f: 16 | for line in f: 17 | genome1, genome2 = (line.strip("[]\n").split(",")) 18 | pairs.append([genome1[1:-1], genome2[2:-1]]) 19 | return pairs 20 | 21 | def get_fasta_file_info(genomes_list): 22 | FASTAFILES_LIST = [el[0] for el in pd.read_csv(genomes_list, header=None).values] 23 | FASTAFILES = {os.path.splitext(os.path.basename(el))[0]:el for el in FASTAFILES_LIST} 24 | FASTAEXT = {os.path.splitext(os.path.basename(el))[0]:os.path.splitext(os.path.basename(el))[1] for el in FASTAFILES_LIST} 25 | FASTAPATH = os.path.dirname(FASTAFILES_LIST[0]) 26 | return FASTAFILES, FASTAEXT, FASTAPATH 27 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools", "wheel"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [project] 6 | name = "pling" 7 | version = "2.0.0" 8 | description = "Pling computes the rearrangement distance between plasmids" 9 | authors = [{name = "Daria Frolova", email = "daria@ebi.ac.uk"}, {name = "Leandro Lima", email = "leandro@ebi.ac.uk"}] 10 | license = {text = "MIT"} 11 | readme = "README.md" 12 | keywords = ["Plasmids", "Comparative genomics", "Genome rearrangement", "DCJ-indel distance"] 13 | requires-python = ">=3.9,<3.12" 14 | 15 | [project.urls] 16 | Homepage = "https://github.com/iqbal-lab-org/pling" 17 | 18 | [project.scripts] 19 | pling = 'pling.run_pling:main' 20 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | if __name__ == "__main__": 3 | setup() 4 | -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/__init__.py -------------------------------------------------------------------------------- /tests/dcj_snakemake/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/dcj_snakemake/__init__.py -------------------------------------------------------------------------------- /tests/dcj_snakemake/test_glpk_sol_to_gurobi_sol.py: -------------------------------------------------------------------------------- 1 | from unittest import TestCase 2 | from pling.dcj_snakemake.glpk_sol_to_gurobi_sol import glpk_sol_to_gurobi_sol 3 | from tests.utils import * 4 | 5 | 6 | class Test_glpk_sol_to_gurobi_sol(TestCase): 7 | def test_glpk_sol_to_gurobi_sol_test_case_short(self): 8 | with open("tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_1/glpk.sol.txt") as input_fh, \ 9 | open("tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_1/glpk_to_gurobi.sol.txt", "w") as output_fh: 10 | glpk_sol_to_gurobi_sol(input_fh, output_fh) 11 | assert_files_are_identical( 12 | "tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_1/glpk_to_gurobi.sol.txt", 13 | "tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_1/gurobi.sol") 14 | 15 | def test_glpk_sol_to_gurobi_sol_test_case_long(self): 16 | with open("tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_2/glpk.sol.txt") as input_fh, \ 17 | open("tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_2/glpk_to_gurobi.sol.txt", "w") as output_fh: 18 | glpk_sol_to_gurobi_sol(input_fh, output_fh) 19 | assert_files_are_identical( 20 | "tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_2/glpk_to_gurobi.sol.txt", 21 | "tests/dcj_snakemake/test_cases/glpk_sol_to_gurobi_sol/test_case_2/gurobi.sol") -------------------------------------------------------------------------------- /tests/integration_test/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/integration_test/__init__.py -------------------------------------------------------------------------------- /tests/integration_test/data/.gitignore: -------------------------------------------------------------------------------- 1 | out_* -------------------------------------------------------------------------------- /tests/integration_test/data/all_plasmids_distances.align.truth.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | CP057418.1 NZ_CP027199.1 21 3 | CP057418.1 NZ_LR882977.1 15 4 | NZ_CP027199.1 NZ_LR882977.1 18 5 | -------------------------------------------------------------------------------- /tests/integration_test/data/all_plasmids_distances.anno.truth.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP027199.1 CP057418.1 18 3 | NZ_LR882977.1 CP057418.1 14 4 | NZ_LR882977.1 NZ_CP027199.1 16 5 | -------------------------------------------------------------------------------- /tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f: 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AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS 3 | -------------------------------------------------------------------------------- /tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress: -------------------------------------------------------------------------------- 1 | #taxgroup protein_accession protein_gi 2 | Escherichia AAA21095.1 151858 3 | -------------------------------------------------------------------------------- /tests/integration_test/data/bakta_db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab: -------------------------------------------------------------------------------- 1 | #taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name 2 | Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A 3 | 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TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA 3 | >ORI10010003 4 | GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | Rfam:RF00001 GO:0003735 2 | -------------------------------------------------------------------------------- /tests/integration_test/data/bakta_db/sorf.dmnd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/integration_test/data/bakta_db/sorf.dmnd -------------------------------------------------------------------------------- /tests/integration_test/data/bakta_db/version.json: -------------------------------------------------------------------------------- 1 | { 2 | "date": "2023-02-20", 3 | "major": 5, 4 | "minor": 0, 5 | "type": "full", 6 | "dependencies": [ 7 | { 8 | "name": "AMRFinderPlus", 9 | "release": "2020-09-22.2" 10 | }, 11 | { 12 | "name": "COG", 13 | "release": "2014" 14 | }, 15 | { 16 | "name": "DoriC", 17 | "release": "10" 18 | }, 19 | { 20 | "name": "ISFinder", 21 | "release": "2019-09-25" 22 | }, 23 | { 24 | "name": "Mob-suite", 25 | "release": "2.0" 26 | }, 27 | { 28 | "name": "Pfam", 29 | "release": "33.1" 30 | }, 31 | { 32 | "name": "RefSeq", 33 | "release": "r202" 34 | }, 35 | { 36 | "name": "Rfam", 37 | "release": "14.2" 38 | }, 39 | { 40 | "name": "UniProtKB/Swiss-Prot", 41 | "release": "2020_04" 42 | } 43 | ], 44 | "experts": [ 45 | { 46 | "name": "AMRFinderPlus", 47 | "release": "3.10.1" 48 | }, 49 | { 50 | "name": "NCBI BlastRules", 51 | "release": "4.0" 52 | } 53 | ] 54 | } 55 | -------------------------------------------------------------------------------- /tests/integration_test/data/incy_list_4.txt: -------------------------------------------------------------------------------- 1 | tests/integration_test/data/CP057418.1.fna 2 | tests/integration_test/data/NZ_CP027199.1.fna 3 | tests/integration_test/data/NZ_LR882977.1.fna 4 | tests/integration_test/data/NZ_MF510423.1.fna 5 | -------------------------------------------------------------------------------- /tests/integration_test/test_integration_test.py: -------------------------------------------------------------------------------- 1 | from argparse import Namespace 2 | from unittest import TestCase 3 | from pling import run_pling 4 | from tests.utils import * 5 | 6 | 7 | class Test_Pling_end_to_end(TestCase): 8 | def read_file(self, path): 9 | """Helper method to read a file.""" 10 | with open(path, "rb") as f: 11 | return f.read() 12 | 13 | def assert_files_are_identical(self, path_to_first_file, path_to_second_file): 14 | first_file_content = self.read_file(path_to_first_file) 15 | second_file_content = self.read_file(path_to_second_file) 16 | self.assertEqual(first_file_content, second_file_content) 17 | 18 | def test_pling_align_end_to_end(self): 19 | args = Namespace( 20 | genomes_list='tests/integration_test/data/incy_list_4.txt', 21 | output_dir='tests/integration_test/data/out_align', 22 | integerisation='align', 23 | unimog=None, 24 | containment_distance=0.6, 25 | dcj=4, 26 | identity=80, 27 | min_indel_size=200, 28 | bh_connectivity=10, 29 | bh_neighbours_edge_density=0.2, 30 | small_subcommunity_size_threshold=4, 31 | plasmid_metadata=None, 32 | cores=2, 33 | storetmp=False, 34 | forceall=True, 35 | ilp_solver="GLPK", 36 | timelimit=None, 37 | resources=None, 38 | profile=None, 39 | batch_size=50, 40 | sourmash=False, 41 | sourmash_threshold=0.85, 42 | topology=None, 43 | regions=False, 44 | output_type="html" 45 | ) 46 | run_pling.pling(args) 47 | 48 | assert_files_are_identical( 49 | "tests/integration_test/data/out_align/all_plasmids_distances.tsv", 50 | "tests/integration_test/data/all_plasmids_distances.align.truth.tsv", 51 | ) 52 | 53 | if __name__ == '__main__': 54 | unittest.main() 55 | -------------------------------------------------------------------------------- /tests/unimog_tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/__init__.py -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/all_plasmids_distances.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reference reverse 0 3 | reference 3_dup 1 4 | reference outlier 2 5 | reference 2_dup_3_dup 2 6 | reference 3_dup_w_inverse 2 7 | reference reference_2 2 8 | reference del_rearrange 2 9 | reference inversion 2 10 | reference dup_and_inverse 2 11 | reference inverse_block 2 12 | reverse 3_dup 1 13 | reverse outlier 2 14 | reverse 2_dup_3_dup 2 15 | reverse 3_dup_w_inverse 2 16 | reverse reference_2 2 17 | reverse del_rearrange 2 18 | reverse inversion 2 19 | reverse dup_and_inverse 2 20 | reverse inverse_block 2 21 | 3_dup outlier 2 22 | 3_dup 2_dup_3_dup 1 23 | 3_dup 3_dup_w_inverse 1 24 | 3_dup reference_2 3 25 | 3_dup del_rearrange 2 26 | 3_dup inversion 3 27 | 3_dup dup_and_inverse 3 28 | 3_dup inverse_block 3 29 | outlier 2_dup_3_dup 2 30 | outlier 3_dup_w_inverse 2 31 | outlier reference_2 2 32 | outlier del_rearrange 2 33 | outlier inversion 2 34 | outlier dup_and_inverse 2 35 | outlier inverse_block 2 36 | 2_dup_3_dup 3_dup_w_inverse 2 37 | 2_dup_3_dup reference_2 3 38 | 2_dup_3_dup del_rearrange 2 39 | 2_dup_3_dup inversion 3 40 | 2_dup_3_dup dup_and_inverse 3 41 | 2_dup_3_dup inverse_block 3 42 | 3_dup_w_inverse reference_2 3 43 | 3_dup_w_inverse del_rearrange 2 44 | 3_dup_w_inverse inversion 3 45 | 3_dup_w_inverse dup_and_inverse 3 46 | 3_dup_w_inverse inverse_block 3 47 | reference_2 del_rearrange 3 48 | reference_2 inversion 1 49 | reference_2 dup_and_inverse 2 50 | reference_2 inverse_block 1 51 | del_rearrange inversion 3 52 | del_rearrange dup_and_inverse 3 53 | del_rearrange inverse_block 3 54 | inversion dup_and_inverse 1 55 | inversion inverse_block 0 56 | dup_and_inverse inverse_block 1 57 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/.snakemake_timestamp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/.snakemake_timestamp -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_0.txt: -------------------------------------------------------------------------------- 1 | ['reference', 'reverse'] 2 | ['reference', '3_dup'] 3 | ['reference', 'outlier'] 4 | ['reference', '2_dup_3_dup'] 5 | ['reference', '3_dup_w_inverse'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_1.txt: -------------------------------------------------------------------------------- 1 | ['reference', 'reference_2'] 2 | ['reference', 'del_rearrange'] 3 | ['reference', 'inversion'] 4 | ['reference', 'dup_and_inverse'] 5 | ['reference', 'inverse_block'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_10.txt: -------------------------------------------------------------------------------- 1 | ['del_rearrange', 'dup_and_inverse'] 2 | ['del_rearrange', 'inverse_block'] 3 | ['inversion', 'dup_and_inverse'] 4 | ['inversion', 'inverse_block'] 5 | ['dup_and_inverse', 'inverse_block'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_2.txt: -------------------------------------------------------------------------------- 1 | ['reverse', '3_dup'] 2 | ['reverse', 'outlier'] 3 | ['reverse', '2_dup_3_dup'] 4 | ['reverse', '3_dup_w_inverse'] 5 | ['reverse', 'reference_2'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_3.txt: -------------------------------------------------------------------------------- 1 | ['reverse', 'del_rearrange'] 2 | ['reverse', 'inversion'] 3 | ['reverse', 'dup_and_inverse'] 4 | ['reverse', 'inverse_block'] 5 | ['3_dup', 'outlier'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_4.txt: -------------------------------------------------------------------------------- 1 | ['3_dup', '2_dup_3_dup'] 2 | ['3_dup', '3_dup_w_inverse'] 3 | ['3_dup', 'reference_2'] 4 | ['3_dup', 'del_rearrange'] 5 | ['3_dup', 'inversion'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_5.txt: -------------------------------------------------------------------------------- 1 | ['3_dup', 'dup_and_inverse'] 2 | ['3_dup', 'inverse_block'] 3 | ['outlier', '2_dup_3_dup'] 4 | ['outlier', '3_dup_w_inverse'] 5 | ['outlier', 'reference_2'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_6.txt: -------------------------------------------------------------------------------- 1 | ['outlier', 'del_rearrange'] 2 | ['outlier', 'inversion'] 3 | ['outlier', 'dup_and_inverse'] 4 | ['outlier', 'inverse_block'] 5 | ['2_dup_3_dup', '3_dup_w_inverse'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_7.txt: -------------------------------------------------------------------------------- 1 | ['2_dup_3_dup', 'reference_2'] 2 | ['2_dup_3_dup', 'del_rearrange'] 3 | ['2_dup_3_dup', 'inversion'] 4 | ['2_dup_3_dup', 'dup_and_inverse'] 5 | ['2_dup_3_dup', 'inverse_block'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_8.txt: -------------------------------------------------------------------------------- 1 | ['3_dup_w_inverse', 'reference_2'] 2 | ['3_dup_w_inverse', 'del_rearrange'] 3 | ['3_dup_w_inverse', 'inversion'] 4 | ['3_dup_w_inverse', 'dup_and_inverse'] 5 | ['3_dup_w_inverse', 'inverse_block'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batch_9.txt: -------------------------------------------------------------------------------- 1 | ['reference_2', 'del_rearrange'] 2 | ['reference_2', 'inversion'] 3 | ['reference_2', 'dup_and_inverse'] 4 | ['reference_2', 'inverse_block'] 5 | ['del_rearrange', 'inversion'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/batches/batching_info.txt: -------------------------------------------------------------------------------- 1 | 5 2 | 11 -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reference reverse 0.0 3 | reference 3_dup 0.0 4 | reference outlier 1.0 5 | reference 2_dup_3_dup 0.0 6 | reference 3_dup_w_inverse 0.004930966469428033 7 | reference reference_2 0.21055226824457596 8 | reference del_rearrange 0.717948717948718 9 | reference inversion 0.21055226824457596 10 | reference dup_and_inverse 0.21055226824457596 11 | reference inverse_block 0.21055226824457596 12 | reverse 3_dup 0.0 13 | reverse outlier 1.0 14 | reverse 2_dup_3_dup 0.0 15 | reverse 3_dup_w_inverse 0.004930966469428033 16 | reverse reference_2 0.21055226824457596 17 | reverse del_rearrange 0.717948717948718 18 | reverse inversion 0.21055226824457596 19 | reverse dup_and_inverse 0.21055226824457596 20 | reverse inverse_block 0.21055226824457596 21 | 3_dup outlier 1.0 22 | 3_dup 2_dup_3_dup 0.0 23 | 3_dup 3_dup_w_inverse 0.0 24 | 3_dup reference_2 0.45221843003412965 25 | 3_dup del_rearrange 0.8047781569965871 26 | 3_dup inversion 0.45358361774744027 27 | 3_dup dup_and_inverse 0.45358361774744027 28 | 3_dup inverse_block 0.45358361774744027 29 | outlier 2_dup_3_dup 1.0 30 | outlier 3_dup_w_inverse 1.0 31 | outlier reference_2 1.0 32 | outlier del_rearrange 1.0 33 | outlier inversion 1.0 34 | outlier dup_and_inverse 1.0 35 | outlier inverse_block 1.0 36 | 2_dup_3_dup 3_dup_w_inverse 0.0 37 | 2_dup_3_dup reference_2 0.5258493353028064 38 | 2_dup_3_dup del_rearrange 0.819330385344283 39 | 2_dup_3_dup inversion 0.5270310192023634 40 | 2_dup_3_dup dup_and_inverse 0.5270310192023634 41 | 2_dup_3_dup inverse_block 0.5270310192023634 42 | 3_dup_w_inverse reference_2 0.4621160409556314 43 | 3_dup_w_inverse del_rearrange 0.8081911262798634 44 | 3_dup_w_inverse inversion 0.4621160409556314 45 | 3_dup_w_inverse dup_and_inverse 0.4621160409556314 46 | 3_dup_w_inverse inverse_block 0.4621160409556314 47 | reference_2 del_rearrange 0.0 48 | reference_2 inversion 0.004799616030717546 49 | reference_2 dup_and_inverse 0.004799616030717546 50 | reference_2 inverse_block 0.004799616030717546 51 | del_rearrange inversion 0.006317119393556503 52 | del_rearrange dup_and_inverse 0.006317119393556503 53 | del_rearrange inverse_block 0.006317119393556503 54 | inversion dup_and_inverse 0.0 55 | inversion inverse_block 0.002399808015358773 56 | dup_and_inverse inverse_block 0.0 57 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/containment_communities/.snakemake_timestamp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/containment_communities/.snakemake_timestamp -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/containment_communities/objects/communities.pkl: 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Communities visualisation

11 | 12 | View community_0 (11 nodes, 55 edges)
13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/containment_communities/visualisations/communities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/containment_communities/visualisations/communities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/containment/containment_communities/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/objects/hub_plasmids.csv: -------------------------------------------------------------------------------- 1 | hub_plasmids 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/objects/subcommunities.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/objects/subcommunities.pkl -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/objects/typing.tsv: -------------------------------------------------------------------------------- 1 | plasmid type 2 | reference community_0_subcommunity_0 3 | reverse community_0_subcommunity_0 4 | 3_dup community_0_subcommunity_0 5 | outlier community_0_subcommunity_0 6 | 2_dup_3_dup community_0_subcommunity_0 7 | 3_dup_w_inverse community_0_subcommunity_0 8 | reference_2 community_0_subcommunity_0 9 | del_rearrange community_0_subcommunity_0 10 | inversion community_0_subcommunity_0 11 | dup_and_inverse community_0_subcommunity_0 12 | inverse_block community_0_subcommunity_0 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | Communities visualisation 6 | 7 | 8 | 9 | 10 |

Communities visualisation

11 | 12 | View community_0 (11 nodes, 55 edges)
13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_555555_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_555555_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777620_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777620_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777777_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777777_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_cc0000_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_cc0000_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_ffffff_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_ffffff_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | subcommunity visualisation 6 | 7 | 8 | 9 | 10 |

subcommunity visualisation

11 | 12 | View community_0_subcommunity_0 (11 nodes, 55 edges)
13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- 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/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_ffffff_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_ffffff_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >reference~reverse:reference 2 | 1 ) 3 | >reference~reverse:reverse 4 | -1 ) 5 | >reference~3_dup:reference 6 | 1 ) 7 | >reference~3_dup:3_dup 8 | 1 2 ) 9 | >reference~outlier:reference 10 | 1 ) 11 | >reference~outlier:outlier 12 | 2 ) 13 | >reference~2_dup_3_dup:reference 14 | 1 2 3 ) 15 | >reference~2_dup_3_dup:2_dup_3_dup 16 | 1 2 2 3 4 ) 17 | >reference~3_dup_w_inverse:reference 18 | 1 2 ) 19 | >reference~3_dup_w_inverse:3_dup_w_inverse 20 | 1 -2 3 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reference~reverse reference 1 1 2029 3 | reverse -1 1 2029 4 | reference~3_dup reference 1 1 2029 5 | 3_dup 1 1 2029 6 | 3_dup 2 2029 2931 7 | reference~outlierreference~2_dup_3_dup reference 1 1 550 8 | reference 2 578 1005 9 | reference 3 1033 2029 10 | 2_dup_3_dup 1 1 550 11 | 2_dup_3_dup 2 578 1005 12 | 2_dup_3_dup 2 1033 1460 13 | 2_dup_3_dup 3 1488 2484 14 | 2_dup_3_dup 4 2484 3386 15 | reference~3_dup_w_inverse reference 1 1 563 16 | reference 2 563 2019 17 | 3_dup_w_inverse 1 1 563 18 | 3_dup_w_inverse -2 563 2019 19 | 3_dup_w_inverse 3 2019 2931 20 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_10_align.unimog: -------------------------------------------------------------------------------- 1 | >del_rearrange~dup_and_inverse:del_rearrange 2 | 1 2 3 ) 3 | >del_rearrange~dup_and_inverse:dup_and_inverse 4 | 4 -2 1 5 3 ) 5 | >del_rearrange~inverse_block:del_rearrange 6 | 1 2 3 ) 7 | >del_rearrange~inverse_block:inverse_block 8 | 2 4 -3 -1 ) 9 | >inversion~dup_and_inverse:inversion 10 | 1 2 3 ) 11 | >inversion~dup_and_inverse:dup_and_inverse 12 | 1 2 2 3 ) 13 | >inversion~inverse_block:inversion 14 | 1 2 ) 15 | >inversion~inverse_block:inverse_block 16 | -1 -2 ) 17 | >dup_and_inverse~inverse_block:dup_and_inverse 18 | 1 3 2 ) 19 | >dup_and_inverse~inverse_block:inverse_block 20 | -1 -2 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_10_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | del_rearrange~dup_and_inverse del_rearrange 1 1 2355 3 | del_rearrange 2 2368 2914 4 | del_rearrange 3 2937 3147 5 | dup_and_inverse 4 1 1025 6 | dup_and_inverse -2 1025 1571 7 | dup_and_inverse 1 1594 3948 8 | dup_and_inverse 5 3948 6322 9 | dup_and_inverse 3 6322 6532 10 | del_rearrange~inverse_block del_rearrange 1 1 2342 11 | del_rearrange 2 2365 2914 12 | del_rearrange 3 2937 3147 13 | inverse_block 2 1 550 14 | inverse_block 4 550 1574 15 | inverse_block -3 1574 1784 16 | inverse_block -1 1807 4148 17 | inversion~dup_and_inverse inversion 1 1 1584 18 | inversion 2 1594 3948 19 | inversion 3 3958 4168 20 | dup_and_inverse 1 1 1584 21 | dup_and_inverse 2 1594 3948 22 | dup_and_inverse 2 3958 6312 23 | dup_and_inverse 3 6322 6532 24 | inversion~inverse_block inversion 1 1 1574 25 | inversion 2 1584 4168 26 | inverse_block -1 1 1574 27 | inverse_block -2 1574 4158 28 | dup_and_inverse~inverse_block dup_and_inverse 1 1 1574 29 | dup_and_inverse 3 1574 3938 30 | dup_and_inverse 2 3938 6532 31 | inverse_block -1 1 1574 32 | inverse_block -2 1574 4168 33 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_1_align.unimog: -------------------------------------------------------------------------------- 1 | >reference~reference_2:reference 2 | 1 3 2 ) 3 | >reference~reference_2:reference_2 4 | 1 2 4 ) 5 | >reference~del_rearrange:reference 6 | 1 2 ) 7 | >reference~del_rearrange:del_rearrange 8 | 3 1 4 ) 9 | >reference~inversion:reference 10 | 1 3 2 ) 11 | >reference~inversion:inversion 12 | -2 -1 4 ) 13 | >reference~dup_and_inverse:reference 14 | 1 3 2 ) 15 | >reference~dup_and_inverse:dup_and_inverse 16 | -2 -1 4 ) 17 | >reference~inverse_block:reference 18 | 1 3 2 ) 19 | >reference~inverse_block:inverse_block 20 | 1 2 4 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_1_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reference~reference_2 reference 1 1 550 3 | reference 3 550 1033 4 | reference 2 1033 2029 5 | reference_2 1 1 550 6 | reference_2 2 578 1574 7 | reference_2 4 1574 4168 8 | reference~del_rearrange reference 1 1 573 9 | reference 2 573 2029 10 | del_rearrange 3 1 2365 11 | del_rearrange 1 2365 2937 12 | del_rearrange 4 2937 3167 13 | reference~inversion reference 1 1 550 14 | reference 3 550 1033 15 | reference 2 1033 2029 16 | inversion -2 1 997 17 | inversion -1 1025 1574 18 | inversion 4 1574 4168 19 | reference~dup_and_inverse reference 1 1 550 20 | reference 3 550 1033 21 | reference 2 1033 2029 22 | dup_and_inverse -2 1 997 23 | dup_and_inverse -1 1025 1574 24 | dup_and_inverse 4 1574 6532 25 | reference~inverse_block reference 1 1 550 26 | reference 3 550 1033 27 | reference 2 1033 2029 28 | inverse_block 1 1 550 29 | inverse_block 2 578 1574 30 | inverse_block 4 1574 4168 31 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_2_align.unimog: -------------------------------------------------------------------------------- 1 | >reverse~3_dup:reverse 2 | 1 ) 3 | >reverse~3_dup:3_dup 4 | -1 2 ) 5 | >reverse~outlier:reverse 6 | 1 ) 7 | >reverse~outlier:outlier 8 | 2 ) 9 | >reverse~2_dup_3_dup:reverse 10 | 1 2 3 ) 11 | >reverse~2_dup_3_dup:2_dup_3_dup 12 | -3 -2 -2 -1 4 ) 13 | >reverse~3_dup_w_inverse:reverse 14 | 1 2 ) 15 | >reverse~3_dup_w_inverse:3_dup_w_inverse 16 | -2 1 3 ) 17 | >reverse~reference_2:reverse 18 | 1 3 2 ) 19 | >reverse~reference_2:reference_2 20 | -2 -1 4 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_2_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reverse~3_dup reverse 1 1 2029 3 | 3_dup -1 1 2029 4 | 3_dup 2 2029 2931 5 | reverse~outlierreverse~2_dup_3_dup reverse 1 1 997 6 | reverse 2 1025 1452 7 | reverse 3 1480 2029 8 | 2_dup_3_dup -3 1 550 9 | 2_dup_3_dup -2 578 1005 10 | 2_dup_3_dup -2 1033 1460 11 | 2_dup_3_dup -1 1488 2484 12 | 2_dup_3_dup 4 2484 3386 13 | reverse~3_dup_w_inverse reverse 1 11 1467 14 | reverse 2 1467 2029 15 | 3_dup_w_inverse -2 1 563 16 | 3_dup_w_inverse 1 563 2019 17 | 3_dup_w_inverse 3 2019 2931 18 | reverse~reference_2 reverse 1 1 997 19 | reverse 3 997 1480 20 | reverse 2 1480 2029 21 | reference_2 -2 1 550 22 | reference_2 -1 578 1574 23 | reference_2 4 1574 4168 24 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_3_align.unimog: -------------------------------------------------------------------------------- 1 | >reverse~del_rearrange:reverse 2 | 2 1 ) 3 | >reverse~del_rearrange:del_rearrange 4 | 3 -1 4 ) 5 | >reverse~inversion:reverse 6 | 1 3 2 ) 7 | >reverse~inversion:inversion 8 | 1 2 4 ) 9 | >reverse~dup_and_inverse:reverse 10 | 1 3 2 ) 11 | >reverse~dup_and_inverse:dup_and_inverse 12 | 1 2 4 ) 13 | >reverse~inverse_block:reverse 14 | 1 3 2 ) 15 | >reverse~inverse_block:inverse_block 16 | -2 -1 4 ) 17 | >3_dup~outlier:3_dup 18 | 1 ) 19 | >3_dup~outlier:outlier 20 | 2 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_3_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reverse~del_rearrange reverse 2 1 1457 3 | reverse 1 1457 2029 4 | del_rearrange 3 1 2365 5 | del_rearrange -1 2365 2937 6 | del_rearrange 4 2937 3167 7 | reverse~inversion reverse 1 1 997 8 | reverse 3 997 1480 9 | reverse 2 1480 2029 10 | inversion 1 1 997 11 | inversion 2 1025 1574 12 | inversion 4 1574 4168 13 | reverse~dup_and_inverse reverse 1 1 997 14 | reverse 3 997 1480 15 | reverse 2 1480 2029 16 | dup_and_inverse 1 1 997 17 | dup_and_inverse 2 1025 1574 18 | dup_and_inverse 4 1574 6532 19 | reverse~inverse_block reverse 1 1 997 20 | reverse 3 997 1480 21 | reverse 2 1480 2029 22 | inverse_block -2 1 550 23 | inverse_block -1 578 1574 24 | inverse_block 4 1574 4168 25 | 3_dup~outlier -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_4_align.unimog: -------------------------------------------------------------------------------- 1 | >3_dup~2_dup_3_dup:3_dup 2 | 1 2 3 ) 3 | >3_dup~2_dup_3_dup:2_dup_3_dup 4 | 1 2 2 3 ) 5 | >3_dup~3_dup_w_inverse:3_dup 6 | 1 2 3 ) 7 | >3_dup~3_dup_w_inverse:3_dup_w_inverse 8 | 1 -2 3 ) 9 | >3_dup~reference_2:3_dup 10 | 1 3 2 4 ) 11 | >3_dup~reference_2:reference_2 12 | 1 2 5 ) 13 | >3_dup~del_rearrange:3_dup 14 | 1 2 ) 15 | >3_dup~del_rearrange:del_rearrange 16 | 3 1 4 ) 17 | >3_dup~inversion:3_dup 18 | 1 3 2 4 ) 19 | >3_dup~inversion:inversion 20 | -2 -1 5 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_4_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 3_dup~2_dup_3_dup 3_dup 1 1 550 3 | 3_dup 2 578 1005 4 | 3_dup 3 1033 2931 5 | 2_dup_3_dup 1 1 550 6 | 2_dup_3_dup 2 578 1005 7 | 2_dup_3_dup 2 1033 1460 8 | 2_dup_3_dup 3 1488 3386 9 | 3_dup~3_dup_w_inverse 3_dup 1 1 563 10 | 3_dup 2 563 2019 11 | 3_dup 3 2019 2931 12 | 3_dup_w_inverse 1 1 563 13 | 3_dup_w_inverse -2 563 2019 14 | 3_dup_w_inverse 3 2019 2931 15 | 3_dup~reference_2 3_dup 1 1 550 16 | 3_dup 3 550 1033 17 | 3_dup 2 1033 2033 18 | 3_dup 4 2033 2931 19 | reference_2 1 1 550 20 | reference_2 2 578 1578 21 | reference_2 5 1578 4168 22 | 3_dup~del_rearrange 3_dup 1 1 573 23 | 3_dup 2 573 2931 24 | del_rearrange 3 1 2365 25 | del_rearrange 1 2365 2937 26 | del_rearrange 4 2937 3167 27 | 3_dup~inversion 3_dup 1 1 550 28 | 3_dup 3 550 1033 29 | 3_dup 2 1033 2029 30 | 3_dup 4 2029 2931 31 | inversion -2 1 997 32 | inversion -1 1025 1574 33 | inversion 5 1574 4168 34 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_5_align.unimog: -------------------------------------------------------------------------------- 1 | >3_dup~dup_and_inverse:3_dup 2 | 1 3 2 4 ) 3 | >3_dup~dup_and_inverse:dup_and_inverse 4 | -2 -1 5 ) 5 | >3_dup~inverse_block:3_dup 6 | 1 3 2 4 ) 7 | >3_dup~inverse_block:inverse_block 8 | 1 2 5 ) 9 | >outlier~2_dup_3_dup:outlier 10 | 1 ) 11 | >outlier~2_dup_3_dup:2_dup_3_dup 12 | 2 ) 13 | >outlier~3_dup_w_inverse:outlier 14 | 1 ) 15 | >outlier~3_dup_w_inverse:3_dup_w_inverse 16 | 2 ) 17 | >outlier~reference_2:outlier 18 | 1 ) 19 | >outlier~reference_2:reference_2 20 | 2 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_5_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 3_dup~dup_and_inverse 3_dup 1 1 550 3 | 3_dup 3 550 1033 4 | 3_dup 2 1033 2029 5 | 3_dup 4 2029 2931 6 | dup_and_inverse -2 1 997 7 | dup_and_inverse -1 1025 1574 8 | dup_and_inverse 5 1574 6532 9 | 3_dup~inverse_block 3_dup 1 1 550 10 | 3_dup 3 550 1033 11 | 3_dup 2 1033 2029 12 | 3_dup 4 2029 2931 13 | inverse_block 1 1 550 14 | inverse_block 2 578 1574 15 | inverse_block 5 1574 4168 16 | outlier~2_dup_3_dupoutlier~3_dup_w_inverseoutlier~reference_2 -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_6_align.unimog: -------------------------------------------------------------------------------- 1 | >outlier~del_rearrange:outlier 2 | 1 ) 3 | >outlier~del_rearrange:del_rearrange 4 | 2 ) 5 | >outlier~inversion:outlier 6 | 1 ) 7 | >outlier~inversion:inversion 8 | 2 ) 9 | >outlier~dup_and_inverse:outlier 10 | 1 ) 11 | >outlier~dup_and_inverse:dup_and_inverse 12 | 2 ) 13 | >outlier~inverse_block:outlier 14 | 1 ) 15 | >outlier~inverse_block:inverse_block 16 | 2 ) 17 | >2_dup_3_dup~3_dup_w_inverse:2_dup_3_dup 18 | 1 4 2 3 ) 19 | >2_dup_3_dup~3_dup_w_inverse:3_dup_w_inverse 20 | 1 -2 3 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_6_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | outlier~del_rearrangeoutlier~inversionoutlier~dup_and_inverseoutlier~inverse_block2_dup_3_dup~3_dup_w_inverse 2_dup_3_dup 1 1 563 3 | 2_dup_3_dup 4 563 1018 4 | 2_dup_3_dup 2 1018 2474 5 | 2_dup_3_dup 3 2474 3386 6 | 3_dup_w_inverse 1 1 563 7 | 3_dup_w_inverse -2 563 2019 8 | 3_dup_w_inverse 3 2019 2931 9 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_7_align.unimog: -------------------------------------------------------------------------------- 1 | >2_dup_3_dup~reference_2:2_dup_3_dup 2 | 1 3 2 4 ) 3 | >2_dup_3_dup~reference_2:reference_2 4 | 1 2 5 ) 5 | >2_dup_3_dup~del_rearrange:2_dup_3_dup 6 | 1 2 ) 7 | >2_dup_3_dup~del_rearrange:del_rearrange 8 | 3 1 4 ) 9 | >2_dup_3_dup~inversion:2_dup_3_dup 10 | 1 3 2 4 ) 11 | >2_dup_3_dup~inversion:inversion 12 | -2 -1 5 ) 13 | >2_dup_3_dup~dup_and_inverse:2_dup_3_dup 14 | 1 3 2 4 ) 15 | >2_dup_3_dup~dup_and_inverse:dup_and_inverse 16 | -2 -1 5 ) 17 | >2_dup_3_dup~inverse_block:2_dup_3_dup 18 | 1 3 2 4 ) 19 | >2_dup_3_dup~inverse_block:inverse_block 20 | 1 2 5 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_7_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 2_dup_3_dup~reference_2 2_dup_3_dup 1 1 550 3 | 2_dup_3_dup 3 550 1488 4 | 2_dup_3_dup 2 1488 2488 5 | 2_dup_3_dup 4 2488 3386 6 | reference_2 1 1 550 7 | reference_2 2 578 1578 8 | reference_2 5 1578 4168 9 | 2_dup_3_dup~del_rearrange 2_dup_3_dup 1 1 573 10 | 2_dup_3_dup 2 573 3386 11 | del_rearrange 3 1 2365 12 | del_rearrange 1 2365 2937 13 | del_rearrange 4 2937 3167 14 | 2_dup_3_dup~inversion 2_dup_3_dup 1 1 550 15 | 2_dup_3_dup 3 550 1488 16 | 2_dup_3_dup 2 1488 2484 17 | 2_dup_3_dup 4 2484 3386 18 | inversion -2 1 997 19 | inversion -1 1025 1574 20 | inversion 5 1574 4168 21 | 2_dup_3_dup~dup_and_inverse 2_dup_3_dup 1 1 550 22 | 2_dup_3_dup 3 550 1488 23 | 2_dup_3_dup 2 1488 2484 24 | 2_dup_3_dup 4 2484 3386 25 | dup_and_inverse -2 1 997 26 | dup_and_inverse -1 1025 1574 27 | dup_and_inverse 5 1574 6532 28 | 2_dup_3_dup~inverse_block 2_dup_3_dup 1 1 550 29 | 2_dup_3_dup 3 550 1488 30 | 2_dup_3_dup 2 1488 2484 31 | 2_dup_3_dup 4 2484 3386 32 | inverse_block 1 1 550 33 | inverse_block 2 578 1574 34 | inverse_block 5 1574 4168 35 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_8_align.unimog: -------------------------------------------------------------------------------- 1 | >3_dup_w_inverse~reference_2:3_dup_w_inverse 2 | 1 2 3 ) 3 | >3_dup_w_inverse~reference_2:reference_2 4 | 1 -2 4 ) 5 | >3_dup_w_inverse~del_rearrange:3_dup_w_inverse 6 | 1 2 ) 7 | >3_dup_w_inverse~del_rearrange:del_rearrange 8 | 3 1 4 ) 9 | >3_dup_w_inverse~inversion:3_dup_w_inverse 10 | 1 2 3 ) 11 | >3_dup_w_inverse~inversion:inversion 12 | 2 -1 4 ) 13 | >3_dup_w_inverse~dup_and_inverse:3_dup_w_inverse 14 | 1 2 3 ) 15 | >3_dup_w_inverse~dup_and_inverse:dup_and_inverse 16 | 2 -1 4 ) 17 | >3_dup_w_inverse~inverse_block:3_dup_w_inverse 18 | 1 2 3 ) 19 | >3_dup_w_inverse~inverse_block:inverse_block 20 | 1 -2 4 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_8_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 3_dup_w_inverse~reference_2 3_dup_w_inverse 1 1 550 3 | 3_dup_w_inverse 2 563 1564 4 | 3_dup_w_inverse 3 1564 2931 5 | reference_2 1 1 550 6 | reference_2 -2 563 1564 7 | reference_2 4 1564 4168 8 | 3_dup_w_inverse~del_rearrange 3_dup_w_inverse 1 1 563 9 | 3_dup_w_inverse 2 563 2931 10 | del_rearrange 3 1 2365 11 | del_rearrange 1 2365 2927 12 | del_rearrange 4 2927 3167 13 | 3_dup_w_inverse~inversion 3_dup_w_inverse 1 1 550 14 | 3_dup_w_inverse 2 563 1564 15 | 3_dup_w_inverse 3 1564 2931 16 | inversion 2 11 1012 17 | inversion -1 1025 1574 18 | inversion 4 1574 4168 19 | 3_dup_w_inverse~dup_and_inverse 3_dup_w_inverse 1 1 550 20 | 3_dup_w_inverse 2 563 1564 21 | 3_dup_w_inverse 3 1564 2931 22 | dup_and_inverse 2 11 1012 23 | dup_and_inverse -1 1025 1574 24 | dup_and_inverse 4 1574 6532 25 | 3_dup_w_inverse~inverse_block 3_dup_w_inverse 1 1 550 26 | 3_dup_w_inverse 2 563 1564 27 | 3_dup_w_inverse 3 1564 2931 28 | inverse_block 1 1 550 29 | inverse_block -2 563 1564 30 | inverse_block 4 1564 4168 31 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_9_align.unimog: -------------------------------------------------------------------------------- 1 | >reference_2~del_rearrange:reference_2 2 | 1 4 2 3 ) 3 | >reference_2~del_rearrange:del_rearrange 4 | 2 1 3 ) 5 | >reference_2~inversion:reference_2 6 | 1 2 ) 7 | >reference_2~inversion:inversion 8 | -1 2 ) 9 | >reference_2~dup_and_inverse:reference_2 10 | 1 2 ) 11 | >reference_2~dup_and_inverse:dup_and_inverse 12 | -1 3 2 ) 13 | >reference_2~inverse_block:reference_2 14 | 1 2 ) 15 | >reference_2~inverse_block:inverse_block 16 | 1 -2 ) 17 | >del_rearrange~inversion:del_rearrange 18 | 1 2 3 ) 19 | >del_rearrange~inversion:inversion 20 | 4 -2 1 3 ) 21 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/containment_1/truth/align/unimogs/batch_9_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reference_2~del_rearrange reference_2 1 1 550 3 | reference_2 4 550 1574 4 | reference_2 2 1574 3915 5 | reference_2 3 3938 4168 6 | del_rearrange 2 1 2342 7 | del_rearrange 1 2365 2914 8 | del_rearrange 3 2937 3167 9 | reference_2~inversion reference_2 1 1 1564 10 | reference_2 2 1574 4148 11 | inversion -1 11 1574 12 | inversion 2 1594 4168 13 | reference_2~dup_and_inverse reference_2 1 1 1551 14 | reference_2 2 1574 4148 15 | dup_and_inverse -1 24 1574 16 | dup_and_inverse 3 1574 3958 17 | dup_and_inverse 2 3958 6532 18 | reference_2~inverse_block reference_2 1 1 1554 19 | reference_2 2 1574 4148 20 | inverse_block 1 1 1554 21 | inverse_block -2 1574 4148 22 | del_rearrange~inversion del_rearrange 1 1 2342 23 | del_rearrange 2 2365 2914 24 | del_rearrange 3 2937 3147 25 | inversion 4 1 1025 26 | inversion -2 1025 1574 27 | inversion 1 1594 3935 28 | inversion 3 3958 4168 29 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/input/palindrome.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/git_issues/input/fastas/genome_1.fna 2 | tests/unimog_tests/test_cases/git_issues/input/fastas/genome_4.fna 3 | tests/unimog_tests/test_cases/git_issues/input/fastas/genome_8.fna 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/all_plasmids_distances.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | genome_1 genome_4 0 3 | genome_1 genome_8 0 4 | genome_4 genome_8 0 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/batches/.snakemake_timestamp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/batches/.snakemake_timestamp -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/batches/batch_0.txt: -------------------------------------------------------------------------------- 1 | ['genome_1', 'genome_4'] 2 | ['genome_1', 'genome_8'] 3 | ['genome_4', 'genome_8'] 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/batches/batching_info.txt: -------------------------------------------------------------------------------- 1 | 10 2 | 1 -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | genome_1 genome_4 0.0 3 | genome_1 genome_8 0.0 4 | genome_4 genome_8 0.0 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/.snakemake_timestamp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/.snakemake_timestamp -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/objects/communities.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/objects/communities.pkl -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | genome_1 community_0 3 | genome_4 community_0 4 | genome_8 community_0 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | genome_1 genome_4 genome_8 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/objects/plasmid_graph.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/objects/plasmid_graph.pkl -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/containment/containment_communities/visualisations/communities/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | Communities visualisation 6 | 7 | 8 | 9 | 10 |

Communities visualisation

11 | 12 | View community_0 (3 nodes, 3 edges)
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Communities visualisation

11 | 12 | View community_0 (3 nodes, 3 edges)
13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_555555_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_555555_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777620_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777620_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777777_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777777_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_cc0000_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_cc0000_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_ffffff_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_ffffff_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | subcommunity visualisation 6 | 7 | 8 | 9 | 10 |

subcommunity visualisation

11 | 12 | View community_0_subcommunity_0 (3 nodes, 3 edges)
13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- 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/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_ffffff_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_ffffff_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >genome_1~genome_4:genome_1 2 | 1 ) 3 | >genome_1~genome_4:genome_4 4 | -1 ) 5 | >genome_1~genome_8:genome_1 6 | 1 2 ) 7 | >genome_1~genome_8:genome_8 8 | 2 1 ) 9 | >genome_4~genome_8:genome_4 10 | 1 2 ) 11 | >genome_4~genome_8:genome_8 12 | -1 -2 ) 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/git_issues/palindrome/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | genome_1~genome_4 genome_1 1 1 4117 3 | genome_4 -1 1 4117 4 | genome_1~genome_8 genome_1 1 1 2701 5 | genome_1 2 2701 4117 6 | genome_8 2 1 1417 7 | genome_8 1 1417 4117 8 | genome_4~genome_8 genome_4 1 1 1417 9 | genome_4 2 1417 4117 10 | genome_8 -1 1 1417 11 | genome_8 -2 1417 4117 12 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_1.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_MK312248.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP129874.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_10.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/LR890289.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP013657.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_11.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/LR890465.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP054769.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_2.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/CP056587.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/CP055413.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_3.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_MH477636.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP047745.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_4.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP102837.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP019161.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_5.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP006799.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_MW245019.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_6.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP037912.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP069936.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_7.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP070577.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP075435.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_8.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP072977.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NC_006816.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/input/test_9.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_CP042975.1.fna 2 | tests/unimog_tests/test_cases/indel_tests/input/fastas/NZ_MT035874.1.fna 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_1/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_MK312248.1 NZ_CP129874.1 0.5265530961949894 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_1/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_MK312248.1 community_0 3 | NZ_CP129874.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_1/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_MK312248.1 NZ_CP129874.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_1/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_MK312248.1~NZ_CP129874.1:NZ_MK312248.1 2 | 1 19 2 20 3 21 4 22 5 6 7 23 8 9 24 10 11 12 13 25 14 26 15 27 4 16 17 18 ) 3 | >NZ_MK312248.1~NZ_CP129874.1:NZ_CP129874.1 4 | 29 -5 30 -15 31 3 32 14 33 -7 -6 -13 34 -12 -11 -10 35 -9 36 -8 37 4 16 38 2 -1 -18 -17 39 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_1/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | NZ_MK312248.1~NZ_CP129874.1 NZ_MK312248.1 1 1 4691 3 | NZ_MK312248.1 19 4691 13228 4 | NZ_MK312248.1 2 13228 13651 5 | NZ_MK312248.1 20 13651 22788 6 | NZ_MK312248.1 3 22788 23737 7 | NZ_MK312248.1 21 23737 41909 8 | NZ_MK312248.1 4 41909 43262 9 | NZ_MK312248.1 22 43262 49172 10 | NZ_MK312248.1 5 49172 56005 11 | NZ_MK312248.1 6 55996 56294 12 | NZ_MK312248.1 7 56490 56913 13 | NZ_MK312248.1 23 56913 63358 14 | NZ_MK312248.1 8 63358 64089 15 | NZ_MK312248.1 9 64081 64847 16 | NZ_MK312248.1 24 64847 70218 17 | NZ_MK312248.1 10 70218 72176 18 | NZ_MK312248.1 11 72371 81754 19 | NZ_MK312248.1 12 81948 90468 20 | NZ_MK312248.1 13 90462 91214 21 | NZ_MK312248.1 25 91214 92780 22 | NZ_MK312248.1 14 92780 93085 23 | NZ_MK312248.1 26 93085 103201 24 | NZ_MK312248.1 15 103201 104397 25 | NZ_MK312248.1 27 104397 110971 26 | NZ_MK312248.1 4 110971 112410 27 | NZ_MK312248.1 16 112410 115261 28 | NZ_MK312248.1 17 115354 115658 29 | NZ_MK312248.1 18 115854 120731 30 | NZ_CP129874.1 29 1 8135 31 | NZ_CP129874.1 -5 8135 14967 32 | NZ_CP129874.1 30 14967 16434 33 | NZ_CP129874.1 -15 16434 17630 34 | NZ_CP129874.1 31 17630 26632 35 | NZ_CP129874.1 3 26632 27571 36 | NZ_CP129874.1 32 27571 31025 37 | NZ_CP129874.1 14 31025 31330 38 | NZ_CP129874.1 33 31330 36677 39 | NZ_CP129874.1 -7 36677 37100 40 | NZ_CP129874.1 -6 37199 37497 41 | NZ_CP129874.1 -13 37497 38249 42 | NZ_CP129874.1 34 38249 39344 43 | NZ_CP129874.1 -12 39344 47910 44 | NZ_CP129874.1 -11 48007 57490 45 | NZ_CP129874.1 -10 57588 59545 46 | NZ_CP129874.1 35 59545 62954 47 | NZ_CP129874.1 -9 62954 63720 48 | NZ_CP129874.1 36 63720 71832 49 | NZ_CP129874.1 -8 71832 72577 50 | NZ_CP129874.1 37 72577 79011 51 | NZ_CP129874.1 4 79011 80364 52 | NZ_CP129874.1 16 80364 83212 53 | NZ_CP129874.1 38 83212 87393 54 | NZ_CP129874.1 2 87393 87816 55 | NZ_CP129874.1 -1 87915 92605 56 | NZ_CP129874.1 -18 92605 97579 57 | NZ_CP129874.1 -17 97678 97981 58 | NZ_CP129874.1 39 97981 100027 59 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_10/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | LR890289.1 NZ_CP013657.1 0.300219829145449 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_10/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | LR890289.1 community_0 3 | NZ_CP013657.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_10/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | LR890289.1 NZ_CP013657.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_10/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >LR890289.1~NZ_CP013657.1:LR890289.1 2 | 34 1 35 2 3 4 5 6 7 36 8 37 9 38 10 11 39 12 13 40 14 15 41 16 42 17 43 18 19 44 20 21 22 45 23 46 24 47 25 48 26 49 27 50 28 51 29 52 30 31 32 53 33 9 54 ) 3 | >LR890289.1~NZ_CP013657.1:NZ_CP013657.1 4 | -12 -8 56 -1 57 -9 -33 58 -19 59 -18 60 -32 61 -31 62 -30 -29 63 -28 64 -27 -7 6 65 15 11 14 66 -26 67 -25 -24 -23 68 -22 69 -21 70 -20 -9 71 -17 -16 72 10 11 -4 -3 -2 4 5 -13 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_11/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP054769.1 LR890465.1 0.0562722397120502 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_11/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP054769.1 community_0 3 | LR890465.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_11/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP054769.1 LR890465.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_11/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_CP054769.1~LR890465.1:NZ_CP054769.1 2 | 1 2 16 3 17 4 18 5 6 8 7 -6 9 19 10 20 11 12 13 14 15 ) 3 | >NZ_CP054769.1~LR890465.1:LR890465.1 4 | 1 22 2 23 3 4 5 6 -7 24 8 25 -6 9 26 10 11 12 12 13 14 14 15 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_11/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | NZ_CP054769.1~LR890465.1 NZ_CP054769.1 1 1 12705 3 | NZ_CP054769.1 2 12696 18655 4 | NZ_CP054769.1 16 18655 24717 5 | NZ_CP054769.1 3 24717 32410 6 | NZ_CP054769.1 17 32410 33738 7 | NZ_CP054769.1 4 33738 34319 8 | NZ_CP054769.1 18 34319 35523 9 | NZ_CP054769.1 5 35523 42961 10 | NZ_CP054769.1 6 42961 43734 11 | NZ_CP054769.1 8 43733 76605 12 | NZ_CP054769.1 7 76605 78941 13 | NZ_CP054769.1 -6 78941 79714 14 | NZ_CP054769.1 9 79714 81375 15 | NZ_CP054769.1 19 81375 82570 16 | NZ_CP054769.1 10 82570 87194 17 | NZ_CP054769.1 20 87194 88398 18 | NZ_CP054769.1 11 88398 175809 19 | NZ_CP054769.1 12 175875 176229 20 | NZ_CP054769.1 13 176295 178144 21 | NZ_CP054769.1 14 178146 191864 22 | NZ_CP054769.1 15 191864 195035 23 | LR890465.1 1 1 12699 24 | LR890465.1 22 12699 13755 25 | LR890465.1 2 13755 19714 26 | LR890465.1 23 19714 44203 27 | LR890465.1 3 44203 51896 28 | LR890465.1 4 51897 52478 29 | LR890465.1 5 52482 59920 30 | LR890465.1 6 59920 60693 31 | LR890465.1 -7 60693 63029 32 | LR890465.1 24 63029 68118 33 | LR890465.1 8 68118 100990 34 | LR890465.1 25 100990 104984 35 | LR890465.1 -6 104984 105757 36 | LR890465.1 9 105757 107418 37 | LR890465.1 26 107418 122401 38 | LR890465.1 10 122401 127026 39 | LR890465.1 11 127030 214475 40 | LR890465.1 12 214541 214895 41 | LR890465.1 12 214961 215188 42 | LR890465.1 13 215338 217187 43 | LR890465.1 14 217189 230977 44 | LR890465.1 14 217190 230918 45 | LR890465.1 15 230918 233933 46 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_2/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | CP056587.1 CP055413.1 0.39788832415213404 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_2/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | CP056587.1 community_0 3 | CP055413.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_2/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | CP056587.1 CP055413.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_2/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >CP056587.1~CP055413.1:CP056587.1 2 | 31 1 2 32 3 33 4 5 6 34 7 35 -5 8 36 9 37 10 38 8 39 11 40 12 13 41 14 42 15 16 17 18 19 43 20 44 21 22 23 45 24 46 25 47 26 27 48 28 29 49 -12 50 30 ) 3 | >CP056587.1~CP055413.1:CP055413.1 4 | 54 -27 55 -25 56 -14 57 -13 58 -26 59 24 28 60 -30 20 61 -21 -19 62 -18 -11 -17 -16 -15 63 -2 64 -7 -6 -5 8 65 -23 66 -22 9 67 8 68 1 10 3 69 29 70 12 71 -4 72 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_3/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_MH477636.1 NZ_CP047745.1 0.4423384943940203 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_3/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_MH477636.1 community_0 3 | NZ_CP047745.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_3/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_MH477636.1 NZ_CP047745.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_3/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_MH477636.1~NZ_CP047745.1:NZ_MH477636.1 2 | 1 12 2 3 13 4 14 5 15 6 7 16 8 17 9 18 10 19 11 ) 3 | >NZ_MH477636.1~NZ_CP047745.1:NZ_CP047745.1 4 | 7 20 8 21 -10 22 -3 23 5 24 -2 25 -1 -11 26 4 9 27 6 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_3/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | NZ_MH477636.1~NZ_CP047745.1 NZ_MH477636.1 1 1 958 3 | NZ_MH477636.1 12 958 1334 4 | NZ_MH477636.1 2 1334 11910 5 | NZ_MH477636.1 3 11910 13696 6 | NZ_MH477636.1 13 13696 18115 7 | NZ_MH477636.1 4 18115 19233 8 | NZ_MH477636.1 14 19233 21757 9 | NZ_MH477636.1 5 21757 22188 10 | NZ_MH477636.1 15 22188 27318 11 | NZ_MH477636.1 6 27318 27760 12 | NZ_MH477636.1 7 27760 28634 13 | NZ_MH477636.1 16 28634 29196 14 | NZ_MH477636.1 8 29196 30119 15 | NZ_MH477636.1 17 30119 104442 16 | NZ_MH477636.1 9 104442 105263 17 | NZ_MH477636.1 18 105263 140851 18 | NZ_MH477636.1 10 140851 141618 19 | NZ_MH477636.1 19 141618 161771 20 | NZ_MH477636.1 11 161771 163589 21 | NZ_CP047745.1 7 1 875 22 | NZ_CP047745.1 20 875 3238 23 | NZ_CP047745.1 8 3238 4161 24 | NZ_CP047745.1 21 4161 4943 25 | NZ_CP047745.1 -10 4943 5709 26 | NZ_CP047745.1 22 5709 9715 27 | NZ_CP047745.1 -3 9715 11501 28 | NZ_CP047745.1 23 11501 12475 29 | NZ_CP047745.1 5 12475 12906 30 | NZ_CP047745.1 24 12906 13870 31 | NZ_CP047745.1 -2 13870 24590 32 | NZ_CP047745.1 25 24590 24823 33 | NZ_CP047745.1 -1 24823 25780 34 | NZ_CP047745.1 -11 25780 27598 35 | NZ_CP047745.1 26 27598 28819 36 | NZ_CP047745.1 4 28819 29937 37 | NZ_CP047745.1 9 29938 30759 38 | NZ_CP047745.1 27 30759 37019 39 | NZ_CP047745.1 6 37019 37461 40 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_4/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP102837.1 NZ_CP019161.1 0.45683174515207026 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_4/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP102837.1 community_0 3 | NZ_CP019161.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_4/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP102837.1 NZ_CP019161.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_4/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_CP102837.1~NZ_CP019161.1:NZ_CP102837.1 2 | 26 6 27 -2 13 28 12 29 8 30 11 7 5 31 4 3 2 1 25 32 24 33 23 22 21 34 20 35 19 36 16 37 17 18 15 38 14 39 10 40 9 41 -7 42 ) 3 | >NZ_CP102837.1~NZ_CP019161.1:NZ_CP019161.1 4 | -1 -2 45 -3 46 -4 47 -5 48 -6 49 -7 50 8 51 -9 52 -10 53 11 54 -12 55 -13 56 -14 57 -15 58 16 59 17 17 18 60 -19 -20 -21 -22 61 -23 -24 -25 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_5/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP006799.1 NZ_MW245019.1 0.31148564955482394 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_5/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP006799.1 community_0 3 | NZ_MW245019.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_5/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP006799.1 NZ_MW245019.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_5/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_CP006799.1~NZ_MW245019.1:NZ_CP006799.1 2 | 21 31 38 33 28 39 17 40 18 19 41 23 42 24 43 25 26 44 35 36 45 27 22 46 32 47 16 48 15 14 13 12 49 34 50 29 51 11 10 8 52 7 53 6 5 4 54 3 55 2 1 37 9 56 30 20 ) 3 | >NZ_CP006799.1~NZ_MW245019.1:NZ_MW245019.1 4 | -1 57 -2 58 -3 -4 59 -5 60 -6 61 -7 62 -8 9 -10 63 -11 64 -12 65 -13 -9 -14 -15 66 -16 67 17 68 18 69 19 70 20 21 71 -22 23 24 25 72 26 -27 73 -28 74 -29 30 31 -32 75 33 -34 76 35 77 36 -37 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_6/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP037912.1 NZ_CP069936.1 0.4700967686834855 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_6/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP037912.1 community_0 3 | NZ_CP069936.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_6/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP037912.1 NZ_CP069936.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_6/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_CP037912.1~NZ_CP069936.1:NZ_CP037912.1 2 | 21 17 22 20 23 19 18 17 24 16 25 15 14 26 13 27 12 28 11 10 29 9 30 8 31 7 32 6 33 5 34 4 35 3 36 2 37 1 38 ) 3 | >NZ_CP037912.1~NZ_CP069936.1:NZ_CP069936.1 4 | 40 -1 -2 41 -3 -4 -5 -6 42 -7 43 -8 -9 -10 44 -11 45 -12 46 -13 47 -14 48 -15 -16 -17 49 -17 -17 -18 50 -19 51 20 52 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_6/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | NZ_CP037912.1~NZ_CP069936.1 NZ_CP037912.1 21 1 11471 3 | NZ_CP037912.1 17 11471 12240 4 | NZ_CP037912.1 22 12240 20064 5 | NZ_CP037912.1 20 20064 21397 6 | NZ_CP037912.1 23 21397 22138 7 | NZ_CP037912.1 19 22138 32160 8 | NZ_CP037912.1 18 32157 42440 9 | NZ_CP037912.1 17 42441 43209 10 | NZ_CP037912.1 24 43209 58760 11 | NZ_CP037912.1 16 58760 61577 12 | NZ_CP037912.1 25 61577 65280 13 | NZ_CP037912.1 15 65280 65641 14 | NZ_CP037912.1 14 65638 76539 15 | NZ_CP037912.1 26 76539 76904 16 | NZ_CP037912.1 13 76904 78717 17 | NZ_CP037912.1 27 78717 79024 18 | NZ_CP037912.1 12 79024 79601 19 | NZ_CP037912.1 28 79601 80618 20 | NZ_CP037912.1 11 80618 85670 21 | NZ_CP037912.1 10 85667 85900 22 | NZ_CP037912.1 29 85900 87478 23 | NZ_CP037912.1 9 87478 92124 24 | NZ_CP037912.1 30 92124 92532 25 | NZ_CP037912.1 8 92532 93592 26 | NZ_CP037912.1 31 93592 94145 27 | NZ_CP037912.1 7 94145 95975 28 | NZ_CP037912.1 32 95975 96246 29 | NZ_CP037912.1 6 96246 97480 30 | NZ_CP037912.1 33 97480 97846 31 | NZ_CP037912.1 5 97846 103559 32 | NZ_CP037912.1 34 103559 104356 33 | NZ_CP037912.1 4 104356 112617 34 | NZ_CP037912.1 35 112617 113632 35 | NZ_CP037912.1 3 113632 115140 36 | NZ_CP037912.1 36 115140 116654 37 | NZ_CP037912.1 2 116654 117934 38 | NZ_CP037912.1 37 117934 120651 39 | NZ_CP037912.1 1 120651 121389 40 | NZ_CP037912.1 38 121389 149305 41 | NZ_CP069936.1 40 1 26231 42 | NZ_CP069936.1 -1 26231 26972 43 | NZ_CP069936.1 -2 26982 28263 44 | NZ_CP069936.1 41 28263 28632 45 | NZ_CP069936.1 -3 28632 30147 46 | NZ_CP069936.1 -4 30195 38438 47 | NZ_CP069936.1 -5 38496 44211 48 | NZ_CP069936.1 -6 44232 45466 49 | NZ_CP069936.1 42 45466 45742 50 | NZ_CP069936.1 -7 45742 47572 51 | NZ_CP069936.1 43 47572 48083 52 | NZ_CP069936.1 -8 48083 49143 53 | NZ_CP069936.1 -9 49216 53857 54 | NZ_CP069936.1 -10 53926 54159 55 | NZ_CP069936.1 44 54159 55469 56 | NZ_CP069936.1 -11 55469 60667 57 | NZ_CP069936.1 45 60667 61832 58 | NZ_CP069936.1 -12 61832 62402 59 | NZ_CP069936.1 46 62402 62708 60 | NZ_CP069936.1 -13 62708 64521 61 | NZ_CP069936.1 47 64521 64885 62 | NZ_CP069936.1 -14 64885 75596 63 | NZ_CP069936.1 48 75596 79336 64 | NZ_CP069936.1 -15 79336 79696 65 | NZ_CP069936.1 -16 79826 82691 66 | NZ_CP069936.1 -17 82753 83521 67 | NZ_CP069936.1 49 83521 88847 68 | NZ_CP069936.1 -17 88847 89615 69 | NZ_CP069936.1 -17 88847 89616 70 | NZ_CP069936.1 -18 89761 100044 71 | NZ_CP069936.1 50 100044 101354 72 | NZ_CP069936.1 -19 101354 111376 73 | NZ_CP069936.1 51 111376 129382 74 | NZ_CP069936.1 20 129382 130715 75 | NZ_CP069936.1 52 130715 134652 76 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_7/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP070577.1 NZ_CP075435.1 0.5973736285610576 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_7/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP070577.1 community_0 3 | NZ_CP075435.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_7/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP070577.1 NZ_CP075435.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_7/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_CP070577.1~NZ_CP075435.1:NZ_CP070577.1 2 | 27 31 4 26 25 32 25 24 33 23 22 34 21 35 20 36 19 18 37 17 38 16 15 39 14 40 2 41 13 42 12 43 11 44 5 45 6 46 7 8 47 3 9 48 10 49 1 30 29 28 ) 3 | >NZ_CP070577.1~NZ_CP075435.1:NZ_CP075435.1 4 | -1 51 2 52 -3 53 -4 54 5 55 6 7 56 8 57 9 10 58 -11 59 -12 60 -13 61 -14 62 -15 63 -16 64 -17 65 -18 66 -19 67 -20 -21 68 -22 69 -23 -24 -25 -26 -27 -28 -29 -30 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_8/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP072977.1 NC_006816.1 0.6166197316420948 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_8/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP072977.1 community_0 3 | NC_006816.1 community_1 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_8/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP072977.1 2 | NC_006816.1 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_8/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/indel_tests/test_8/truth/align/unimogs/batch_0_align.unimog -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_8/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_9/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | NZ_CP042975.1 NZ_MT035874.1 0.4403965672910878 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_9/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | NZ_CP042975.1 community_0 3 | NZ_MT035874.1 community_0 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_9/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | NZ_CP042975.1 NZ_MT035874.1 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_9/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >NZ_CP042975.1~NZ_MT035874.1:NZ_CP042975.1 2 | 18 2 4 1 17 16 19 15 14 13 10 9 8 20 7 5 6 21 3 22 12 23 11 24 ) 3 | >NZ_CP042975.1~NZ_MT035874.1:NZ_MT035874.1 4 | -1 -2 25 -3 4 26 5 27 6 28 -7 29 -8 30 -9 31 -10 32 11 33 12 34 -13 35 -14 -15 -16 -17 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/indel_tests/test_9/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | NZ_CP042975.1~NZ_MT035874.1 NZ_CP042975.1 18 1 5047 3 | NZ_CP042975.1 2 5047 8988 4 | NZ_CP042975.1 4 8997 10054 5 | NZ_CP042975.1 1 10062 24773 6 | NZ_CP042975.1 17 24773 42215 7 | NZ_CP042975.1 16 41645 42384 8 | NZ_CP042975.1 19 42384 42684 9 | NZ_CP042975.1 15 42684 53885 10 | NZ_CP042975.1 14 54062 56851 11 | NZ_CP042975.1 13 56854 83447 12 | NZ_CP042975.1 10 83447 84503 13 | NZ_CP042975.1 9 84503 86903 14 | NZ_CP042975.1 8 86899 91528 15 | NZ_CP042975.1 20 91528 106511 16 | NZ_CP042975.1 7 106511 108980 17 | NZ_CP042975.1 5 108211 112896 18 | NZ_CP042975.1 6 112895 144504 19 | NZ_CP042975.1 21 144504 152958 20 | NZ_CP042975.1 3 152958 153462 21 | NZ_CP042975.1 22 153462 241546 22 | NZ_CP042975.1 12 241546 242850 23 | NZ_CP042975.1 23 242850 269467 24 | NZ_CP042975.1 11 269467 270090 25 | NZ_CP042975.1 24 270090 270777 26 | NZ_MT035874.1 -1 1 14707 27 | NZ_MT035874.1 -2 14716 18658 28 | NZ_MT035874.1 25 18658 63823 29 | NZ_MT035874.1 -3 63823 64327 30 | NZ_MT035874.1 4 64504 65561 31 | NZ_MT035874.1 26 65561 71830 32 | NZ_MT035874.1 5 71830 76516 33 | NZ_MT035874.1 27 76516 77842 34 | NZ_MT035874.1 6 77842 109454 35 | NZ_MT035874.1 28 109454 113295 36 | NZ_MT035874.1 -7 113295 115730 37 | NZ_MT035874.1 29 115730 116925 38 | NZ_MT035874.1 -8 116925 121552 39 | NZ_MT035874.1 30 121552 122748 40 | NZ_MT035874.1 -9 122748 125148 41 | NZ_MT035874.1 31 125148 126828 42 | NZ_MT035874.1 -10 126828 127884 43 | NZ_MT035874.1 32 127884 154264 44 | NZ_MT035874.1 11 154264 154888 45 | NZ_MT035874.1 33 154888 163778 46 | NZ_MT035874.1 12 163778 165083 47 | NZ_MT035874.1 34 165083 168952 48 | NZ_MT035874.1 -13 168952 195521 49 | NZ_MT035874.1 35 195521 196013 50 | NZ_MT035874.1 -14 196013 198795 51 | NZ_MT035874.1 -15 198801 210002 52 | NZ_MT035874.1 -16 210002 210740 53 | NZ_MT035874.1 -17 210381 228159 54 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/input/fastas/outlier.fna: -------------------------------------------------------------------------------- 1 | >outlier 2 | aaaaaaaaaaaaaaaaaaaaa 3 | atggaaacagctgtagcgtactataaagatggtgttccttatgatgataaggggcaggta 4 | atcattactcttttgaatggtaatccagacgggag------tggctctggcggtggtggt 5 | ggaactggaggtagcaaaagtgaaagttctgcagccattcatgccacagctaaatggtct 6 | actgctcaattgaagaaaacgcaggcagaacaggctgcccgagcaaaagctgccgcagaa 7 | gcacaggctaaagcaaaagcaaaccgggatgcgctgactcaacatctgaaggatattgtg 8 | aatgaggcgcttcgccataattccactcatccggaggttattgacctggctcatgccaat 9 | aatgcagcgatgcaggcagaagcagagcggttgcgccttgcaaaagcagaagaaaaagcc 10 | cgtaaagaagcggaagctgcggaaaaggcttttcaggaagcagaacaacgacgtaaagag 11 | atagagaaggagcaggctgaaacagaacgccaattgaaactggctgaggatgaagagaaa 12 | cgcctggcagcattgagtgaagaggcccgagctgtggaggtggcacaaaaaaatcttgct 13 | gctgcacaatctgagctggcgaaagtggatgaagagattaatacgctcaatacccgttta 14 | agctccagtattcatgcccgtgatgcagaaacgaatacgctgtccggaaaacgaaatgag 15 | ttggatcaggcatctgctaaatataaagaactggatgaaagggttaaacttttatctcct 16 | agggcgaatgatccgcttcagagtcgtcctttttttgaggccaccagactacgggcgaga 17 | gctggtgatgagatggaggaaaaacaaaagcaggtaacagcatcagaaacgcgtcttaac 18 | cagattagctctgagataaatggaatccaagaggctatttctcaggctaataataagcga 19 | agtacagcagtttcacgtattcatgatgctgaagataatttgaaaacagcacagactaat 20 | ctcctgaactcgcagattaaggatgctgtggatgcaacagttagcttttatcaaacgcta 21 | tctgaaaaatatggtgaaaaatattcaaaaatggcacaggaacttgctgataaatctaaa 22 | ggtaagaaaatcagcaatgtgaatgaagctctagctgcttttgagaaatacaaggatgta 23 | ttaaataagaaattcagcaaagcagaccgtgatgcaattttcaatgcactggaggcggtt 24 | aagtatgaagactgggctaagcatttagatcagtttgccaagtacttgaagattacggga 25 | catgtttcttttggatatgatgtggtatctgatatcctaaaaattaaggatacaggtgac 26 | tggaagccgctatttcttacattagagaagaaagctgtagatgctggagttagttatgtt 27 | gttgttttactttttagtgtgcttgctggaactacattaggtatctgggggattgctatt 28 | gttacaggcattctatgtgcctttattgataagaataaacttaatactataaatgaggtg 29 | ttgggtatttaa 30 | aaaaaaaaaaaaaaaaaaa 31 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/input/fastas/reference.fna: -------------------------------------------------------------------------------- 1 | >reference 2 | ATGTCAGGTAAAAAAACTATCGTTACTCTGCTCCGGGTATCGCTACTGGCATGCCCGTTA 3 | CTGTTCACGACACCATCGTTTGCAATGATCGACACGCCATCCGTGAAGGTCGGCTTTTCT 4 | CCTGAAGGAAGCGCATCCGCTCTGGTGCTTGACACAATCAACAGTGCGGAAAGCTCCATC 5 | AGGATGATGGCATATTCCTTCACCGACCCGGATGTAATGCATGCGCTGGCAAAAGCGAAA 6 | AAACGCGGAGTGGACGTCCGTATTGTTGTTGATGACAAGGGGAATACGAACCGGGCAAGT 7 | CAGGAAGCGATGAAATATATCAACCTGCTGGACATTCCTCTCCGGACTGTAGATGCCTTC 8 | CCCATCCATCACGACAAAGTCATCATTGTTGACGGAAACACGGTTGAAACTGGCTCCTAT 9 | AACTTCTCTCGTGCTGCTGCACGCAAGAATTCAGAGAATGTCGTTGTGCTCAAGAATATG 10 | CCGGATGTAGCCGCACAATATCTTGAACACTGGCAGGATCGCTGGAATAAGGGTACAGAC 11 | TGGAGACCCTGA 12 | AAAAAAAAAAAAAAAAAAAA 13 | ATGAATACCGAACTGACACTGAATGCCCTGCAGTCCATGAATGCCCAGGAATATGAAGAA 14 | ATCCGTGCTGCGGGAAGCGATATGCGCCGTAATCTCACTCACGAGGTGATGCGTGAAGTG 15 | GACGCACCGGCTAACTGGATGATGAACGGAGAGTATGGCAGCGAGTTCGGGGGCTTTTTC 16 | CCCGTCCAGGTTCGTTTCACGCCAGCCCACGAACGTTTCCACCTGGCATTATGTTCGCCG 17 | GGAGACGTCTCTCAGCTCTGGATGCTGGTTCTGGTGAATGGTGGTGGACAGCCTTTCGCC 18 | GTCGTTCAGGTGCAACATATCTTCACGCCTGCCGCGATCAGTCACACGCTGGCGCTTGCC 19 | GCGACACTGGATGCGCAGGGATACAGTGTTAACGACATCATCCATATCCTGATGGCAGAA 20 | GGAGGTCAGGCATGA 21 | AAAAAAAAAAAAAAAAAAAA 22 | ATGAAAATCTTTATTGATGATGGTTCTACCAACATTAAACTTGCCTGGTTGGAGGATGGT 23 | GACGTGAAAACGTTAATCAGCCCTAACAGCTTTAAACCGGAATGGTCTTTTAGTTTACTG 24 | GATGATGCTGCTCCGGCTAATTACGAGATCGACGGCGAGAAGTTTTCATTTGATCCATTA 25 | AGTGCTGATGCTGTCGTAACGACTGAAACACGCTATCAGTACAGTGATGTGAATGTTGTG 26 | GCCATTCAGCATGCGCTACAGCAGACCGGCCTGAAAGCGCAGCCTGTTGATGTCATCGTC 27 | ACATTGCCGATCTCTGAATACCTTGACGCCAACAATCAGAAAAATAAGCAAAACATTGAA 28 | AGAAAGAAAAAAAATGTGATGCGTGAAGTACGGGTGCAGGGGAGTGATGCATTTGTTATT 29 | CGCAGTGTTTCCGTTCTTCCTGAAAGTATTCCCGCTGGTTTCAGTGTTCTTGCGGGGCTT 30 | GAGGATGATGAATCCCTTTTGATCGTAGATCTCGGTGGTACAACTCTTGATGTGTCGCAT 31 | GTTCGTAGCAAAATGACAGGGATTACAAAAACCTGGTGTGATCCGAATATCGGCGTGTCC 32 | CTGATTACATCCGGGGTTAAGGAACAGATGGCTGTACATGCTAATACAAGAGTGAGCTCA 33 | TTCCAGGCTGACAATATCATTGTGCACCGTAATGAACCTGACTACCTTTCCCGTCGCATT 34 | TATAATGCTGAACAGCGTGAGTCTATCATTAATGTTATCAATGAACGGCAGAAGTTGCTT 35 | ATTAAACGAGTTAATGATGTCATCAGCCGTTTCACCGACTATACACATGTAATGTGTGTT 36 | GGTGGTGGGGCTGAAATTGTGGCCGAGGCTGTGAAGAACCTGACTAAGGTTCCTGATGAG 37 | CGCTTTTATCTGAGCTCATCCCCGCAGTTTGATTTAGTCATGGGAATGATAAAAATGAAA 38 | GGTGGTGTGACTAATGAGTGA 39 | AAAAAAAAAAAAAAAAAAAA 40 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/input/fastas/reverse.fna: -------------------------------------------------------------------------------- 1 | >reverse 2 | TTTTTTTTTTTTTTTTTTTT 3 | TCACTCATTAGTCACACCACCTTTCATTTTTATCATTCCCATGACTAAATCAAACTGCGG 4 | GGATGAGCTCAGATAAAAGCGCTCATCAGGAACCTTAGTCAGGTTCTTCACAGCCTCGGC 5 | CACAATTTCAGCCCCACCACCAACACACATTACATGTGTATAGTCGGTGAAACGGCTGAT 6 | GACATCATTAACTCGTTTAATAAGCAACTTCTGCCGTTCATTGATAACATTAATGATAGA 7 | CTCACGCTGTTCAGCATTATAAATGCGACGGGAAAGGTAGTCAGGTTCATTACGGTGCAC 8 | AATGATATTGTCAGCCTGGAATGAGCTCACTCTTGTATTAGCATGTACAGCCATCTGTTC 9 | CTTAACCCCGGATGTAATCAGGGACACGCCGATATTCGGATCACACCAGGTTTTTGTAAT 10 | CCCTGTCATTTTGCTACGAACATGCGACACATCAAGAGTTGTACCACCGAGATCTACGAT 11 | CAAAAGGGATTCATCATCCTCAAGCCCCGCAAGAACACTGAAACCAGCGGGAATACTTTC 12 | AGGAAGAACGGAAACACTGCGAATAACAAATGCATCACTCCCCTGCACCCGTACTTCACG 13 | CATCACATTTTTTTTCTTTCTTTCAATGTTTTGCTTATTTTTCTGATTGTTGGCGTCAAG 14 | GTATTCAGAGATCGGCAATGTGACGATGACATCAACAGGCTGCGCTTTCAGGCCGGTCTG 15 | CTGTAGCGCATGCTGAATGGCCACAACATTCACATCACTGTACTGATAGCGTGTTTCAGT 16 | CGTTACGACAGCATCAGCACTTAATGGATCAAATGAAAACTTCTCGCCGTCGATCTCGTA 17 | ATTAGCCGGAGCAGCATCATCCAGTAAACTAAAAGACCATTCCGGTTTAAAGCTGTTAGG 18 | GCTGATTAACGTTTTCACGTCACCATCCTCCAACCAGGCAAGTTTAATGTTGGTAGAACC 19 | ATCATCAATAAAGATTTTCAT 20 | TTTTTTTTTTTTTTTTTTTT 21 | TCATGCCTGACCTCCTTCTGCCATCAGGATATGGATGATGTCGTTAACACTGTATCCCTG 22 | CGCATCCAGTGTCGCGGCAAGCGCCAGCGTGTGACTGATCGCGGCAGGCGTGAAGATATG 23 | TTGCACCTGAACGACGGCGAAAGGCTGTCCACCACCATTCACCAGAACCAGCATCCAGAG 24 | CTGAGAGACGTCTCCCGGCGAACATAATGCCAGGTGGAAACGTTCGTGGGCTGGCGTGAA 25 | ACGAACCTGGACGGGGAAAAAGCCCCCGAACTCGCTGCCATACTCTCCGTTCATCATCCA 26 | GTTAGCCGGTGCGTCCACTTCACGCATCACCTCGTGAGTGAGATTACGGCGCATATCGCT 27 | TCCCGCAGCACGGATTTCTTCATATTCCTGGGCATTCATGGACTGCAGGGCATTCAGTGT 28 | CAGTTCGGTATTCAT 29 | TTTTTTTTTTTTTTTTTTTT 30 | TCAGGGTCTCCAGTCTGTACCCTTATTCCAGCGATCCTGCCAGTGTTCAAGATATTGTGC 31 | GGCTACATCCGGCATATTCTTGAGCACAACGACATTCTCTGAATTCTTGCGTGCAGCAGC 32 | ACGAGAGAAGTTATAGGAGCCAGTTTCAACCGTGTTTCCGTCAACAATGATGACTTTGTC 33 | GTGATGGATGGGGAAGGCATCTACAGTCCGGAGAGGAATGTCCAGCAGGTTGATATATTT 34 | CATCGCTTCCTGACTTGCCCGGTTCGTATTCCCCTTGTCATCAACAACAATACGGACGTC 35 | CACTCCGCGTTTTTTCGCTTTTGCCAGCGCATGCATTACATCCGGGTCGGTGAAGGAATA 36 | TGCCATCATCCTGATGGAGCTTTCCGCACTGTTGATTGTGTCAAGCACCAGAGCGGATGC 37 | GCTTCCTTCAGGAGAAAAGCCGACCTTCACGGATGGCGTGTCGATCATTGCAAACGATGG 38 | TGTCGTGAACAGTAACGGGCATGCCAGTAGCGATACCCGGAGCAGAGTAACGATAGTTTT 39 | TTTACCTGACAT 40 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/input/skip.unimog: -------------------------------------------------------------------------------- 1 | >reverse 2 | -2 -3 -1 ) 3 | >reference 4 | 1 3 2 ) 5 | >3_dup 6 | 1 3 2 2 ) 7 | >2_dup_3_dup 8 | 1 3 3 2 2 ) 9 | >3_dup_w_inverse 10 | 1 -2 -3 2 ) 11 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/input/test_1.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/toy_tests/input/fastas/reference.fna 2 | tests/unimog_tests/test_cases/toy_tests/input/fastas/reverse.fna 3 | tests/unimog_tests/test_cases/toy_tests/input/fastas/3_dup.fna 4 | tests/unimog_tests/test_cases/toy_tests/input/fastas/2_dup_3_dup.fna 5 | tests/unimog_tests/test_cases/toy_tests/input/fastas/3_dup_w_inverse.fna 6 | tests/unimog_tests/test_cases/toy_tests/input/fastas/outlier.fna 7 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/input/test_2.txt: -------------------------------------------------------------------------------- 1 | tests/unimog_tests/test_cases/toy_tests/input/fastas/reference.fna 2 | tests/unimog_tests/test_cases/toy_tests/input/fastas/reverse.fna 3 | tests/unimog_tests/test_cases/toy_tests/input/fastas/3_dup.fna 4 | tests/unimog_tests/test_cases/toy_tests/input/fastas/outlier.fna 5 | tests/unimog_tests/test_cases/toy_tests/input/fastas/2_dup_3_dup.fna 6 | tests/unimog_tests/test_cases/toy_tests/input/fastas/3_dup_w_inverse.fna 7 | tests/unimog_tests/test_cases/toy_tests/input/fastas/reference_2.fna 8 | tests/unimog_tests/test_cases/toy_tests/input/fastas/del_rearrange.fna 9 | tests/unimog_tests/test_cases/toy_tests/input/fastas/inversion.fna 10 | tests/unimog_tests/test_cases/toy_tests/input/fastas/dup_and_inverse.fna 11 | tests/unimog_tests/test_cases/toy_tests/input/fastas/inverse_block.fna 12 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/all_plasmids_distances.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reference reverse 0 3 | reference 3_dup 1 4 | reference 2_dup_3_dup 2 5 | reference 3_dup_w_inverse 2 6 | reverse 3_dup 1 7 | reverse 2_dup_3_dup 2 8 | reverse 3_dup_w_inverse 2 9 | 3_dup 2_dup_3_dup 1 10 | 3_dup 3_dup_w_inverse 1 11 | 2_dup_3_dup 3_dup_w_inverse 2 12 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/batches/batch_0.txt: -------------------------------------------------------------------------------- 1 | ['reference', 'reverse'] 2 | ['reference', '3_dup'] 3 | ['reference', '2_dup_3_dup'] 4 | ['reference', '3_dup_w_inverse'] 5 | ['reference', 'outlier'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/batches/batch_1.txt: -------------------------------------------------------------------------------- 1 | ['reverse', '3_dup'] 2 | ['reverse', '2_dup_3_dup'] 3 | ['reverse', '3_dup_w_inverse'] 4 | ['reverse', 'outlier'] 5 | ['3_dup', '2_dup_3_dup'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/batches/batch_2.txt: -------------------------------------------------------------------------------- 1 | ['3_dup', '3_dup_w_inverse'] 2 | ['3_dup', 'outlier'] 3 | ['2_dup_3_dup', '3_dup_w_inverse'] 4 | ['2_dup_3_dup', 'outlier'] 5 | ['3_dup_w_inverse', 'outlier'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/batches/batching_info.txt: -------------------------------------------------------------------------------- 1 | 5 2 | 3 -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reference reverse 0.0 3 | reference 3_dup 0.0 4 | reference 2_dup_3_dup 0.0 5 | reference 3_dup_w_inverse 0.004930966469428033 6 | reference outlier 1.0 7 | reverse 3_dup 0.0 8 | reverse 2_dup_3_dup 0.0 9 | reverse 3_dup_w_inverse 0.004930966469428033 10 | reverse outlier 1.0 11 | 3_dup 2_dup_3_dup 0.0 12 | 3_dup 3_dup_w_inverse 0.0 13 | 3_dup outlier 1.0 14 | 2_dup_3_dup 3_dup_w_inverse 0.0 15 | 2_dup_3_dup outlier 1.0 16 | 3_dup_w_inverse outlier 1.0 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | reference community_0 3 | reverse community_0 4 | 3_dup community_0 5 | 2_dup_3_dup community_0 6 | 3_dup_w_inverse community_0 7 | outlier community_1 8 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | reference reverse 3_dup 2_dup_3_dup 3_dup_w_inverse 2 | outlier 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/dcj_thresh_4_graph/objects/hub_plasmids.csv: -------------------------------------------------------------------------------- 1 | hub_plasmids 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/dcj_thresh_4_graph/objects/typing.tsv: -------------------------------------------------------------------------------- 1 | plasmid type 2 | reference community_0_subcommunity_0 3 | reverse community_0_subcommunity_0 4 | 3_dup community_0_subcommunity_0 5 | 2_dup_3_dup community_0_subcommunity_0 6 | 3_dup_w_inverse community_0_subcommunity_0 7 | outlier community_1_subcommunity_0 8 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >reference~reverse:reference 2 | 1 ) 3 | >reference~reverse:reverse 4 | -1 ) 5 | >reference~3_dup:reference 6 | 1 ) 7 | >reference~3_dup:3_dup 8 | 1 2 ) 9 | >reference~2_dup_3_dup:reference 10 | 1 2 3 ) 11 | >reference~2_dup_3_dup:2_dup_3_dup 12 | 1 2 2 3 4 ) 13 | >reference~3_dup_w_inverse:reference 14 | 1 2 ) 15 | >reference~3_dup_w_inverse:3_dup_w_inverse 16 | 1 -2 3 ) 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reference~reverse reference 1 1 2029 3 | reverse -1 1 2029 4 | reference~3_dup reference 1 1 2029 5 | 3_dup 1 1 2029 6 | 3_dup 2 2029 2931 7 | reference~2_dup_3_dup reference 1 1 550 8 | reference 2 578 1005 9 | reference 3 1033 2029 10 | 2_dup_3_dup 1 1 550 11 | 2_dup_3_dup 2 578 1005 12 | 2_dup_3_dup 2 1033 1460 13 | 2_dup_3_dup 3 1488 2484 14 | 2_dup_3_dup 4 2484 3386 15 | reference~3_dup_w_inverse reference 1 1 563 16 | reference 2 563 2019 17 | 3_dup_w_inverse 1 1 563 18 | 3_dup_w_inverse -2 563 2019 19 | 3_dup_w_inverse 3 2019 2931 20 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/unimogs/batch_1_align.unimog: -------------------------------------------------------------------------------- 1 | >reverse~3_dup:reverse 2 | 1 ) 3 | >reverse~3_dup:3_dup 4 | -1 2 ) 5 | >reverse~2_dup_3_dup:reverse 6 | 1 2 3 ) 7 | >reverse~2_dup_3_dup:2_dup_3_dup 8 | -3 -2 -2 -1 4 ) 9 | >reverse~3_dup_w_inverse:reverse 10 | 1 2 ) 11 | >reverse~3_dup_w_inverse:3_dup_w_inverse 12 | -2 1 3 ) 13 | >3_dup~2_dup_3_dup:3_dup 14 | 1 2 3 ) 15 | >3_dup~2_dup_3_dup:2_dup_3_dup 16 | 1 2 2 3 ) 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/unimogs/batch_1_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reverse~3_dup reverse 1 1 2029 3 | 3_dup -1 1 2029 4 | 3_dup 2 2029 2931 5 | reverse~2_dup_3_dup reverse 1 1 997 6 | reverse 2 1025 1452 7 | reverse 3 1480 2029 8 | 2_dup_3_dup -3 1 550 9 | 2_dup_3_dup -2 578 1005 10 | 2_dup_3_dup -2 1033 1460 11 | 2_dup_3_dup -1 1488 2484 12 | 2_dup_3_dup 4 2484 3386 13 | reverse~3_dup_w_inverse reverse 1 11 1467 14 | reverse 2 1467 2029 15 | 3_dup_w_inverse -2 1 563 16 | 3_dup_w_inverse 1 563 2019 17 | 3_dup_w_inverse 3 2019 2931 18 | 3_dup~2_dup_3_dup 3_dup 1 1 550 19 | 3_dup 2 578 1005 20 | 3_dup 3 1033 2931 21 | 2_dup_3_dup 1 1 550 22 | 2_dup_3_dup 2 578 1005 23 | 2_dup_3_dup 2 1033 1460 24 | 2_dup_3_dup 3 1488 3386 25 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/unimogs/batch_2_align.unimog: -------------------------------------------------------------------------------- 1 | >3_dup~3_dup_w_inverse:3_dup 2 | 1 2 3 ) 3 | >3_dup~3_dup_w_inverse:3_dup_w_inverse 4 | 1 -2 3 ) 5 | >2_dup_3_dup~3_dup_w_inverse:2_dup_3_dup 6 | 1 4 2 3 ) 7 | >2_dup_3_dup~3_dup_w_inverse:3_dup_w_inverse 8 | 1 -2 3 ) 9 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/align/unimogs/batch_2_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 3_dup~3_dup_w_inverse 3_dup 1 1 563 3 | 3_dup 2 563 2019 4 | 3_dup 3 2019 2931 5 | 3_dup_w_inverse 1 1 563 6 | 3_dup_w_inverse -2 563 2019 7 | 3_dup_w_inverse 3 2019 2931 8 | 2_dup_3_dup~3_dup_w_inverse 2_dup_3_dup 1 1 563 9 | 2_dup_3_dup 4 563 1018 10 | 2_dup_3_dup 2 1018 2474 11 | 2_dup_3_dup 3 2474 3386 12 | 3_dup_w_inverse 1 1 563 13 | 3_dup_w_inverse -2 563 2019 14 | 3_dup_w_inverse 3 2019 2931 15 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/all_plasmids_distances.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reference reverse 0 3 | reference 3_dup 1 4 | reference 2_dup_3_dup 1 5 | reference 3_dup_w_inverse 2 6 | reverse 3_dup 1 7 | reverse 2_dup_3_dup 1 8 | reverse 3_dup_w_inverse 2 9 | 3_dup 2_dup_3_dup 1 10 | 3_dup 3_dup_w_inverse 1 11 | 2_dup_3_dup 3_dup_w_inverse 2 12 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/batches/.snakemake_timestamp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/batches/.snakemake_timestamp -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/batches/batch_0.txt: -------------------------------------------------------------------------------- 1 | ['reference', 'reverse'] 2 | ['reference', '3_dup'] 3 | ['reference', '2_dup_3_dup'] 4 | ['reference', '3_dup_w_inverse'] 5 | ['reference', 'outlier'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/batches/batch_1.txt: -------------------------------------------------------------------------------- 1 | ['reverse', '3_dup'] 2 | ['reverse', '2_dup_3_dup'] 3 | ['reverse', '3_dup_w_inverse'] 4 | ['reverse', 'outlier'] 5 | ['3_dup', '2_dup_3_dup'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/batches/batch_2.txt: -------------------------------------------------------------------------------- 1 | ['3_dup', '3_dup_w_inverse'] 2 | ['3_dup', 'outlier'] 3 | ['2_dup_3_dup', '3_dup_w_inverse'] 4 | ['2_dup_3_dup', 'outlier'] 5 | ['3_dup_w_inverse', 'outlier'] 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/batches/batching_info.txt: -------------------------------------------------------------------------------- 1 | 5 2 | 3 -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reference reverse 0.0 3 | reference 3_dup 0.0 4 | reference 2_dup_3_dup 0.0 5 | reference 3_dup_w_inverse 0.004930966469428033 6 | reference outlier 1.0 7 | reverse 3_dup 0.0 8 | reverse 2_dup_3_dup 0.0 9 | reverse 3_dup_w_inverse 0.004930966469428033 10 | reverse outlier 1.0 11 | 3_dup 2_dup_3_dup 0.0 12 | 3_dup 3_dup_w_inverse 0.0 13 | 3_dup outlier 1.0 14 | 2_dup_3_dup 3_dup_w_inverse 0.0 15 | 2_dup_3_dup outlier 1.0 16 | 3_dup_w_inverse outlier 1.0 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/containment_communities/.snakemake_timestamp: -------------------------------------------------------------------------------- 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community 2 | reference community_0 3 | reverse community_0 4 | 3_dup community_0 5 | 2_dup_3_dup community_0 6 | 3_dup_w_inverse community_0 7 | outlier community_1 8 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | reference reverse 3_dup 2_dup_3_dup 3_dup_w_inverse 2 | outlier 3 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/containment_communities/objects/plasmid_graph.pkl: -------------------------------------------------------------------------------- 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Communities visualisation

11 | 12 | View community_0 (5 nodes, 10 edges)
13 | View community_1 (1 nodes, 0 edges)
14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/containment_communities/visualisations/communities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/containment_communities/visualisations/communities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/containment/containment_communities/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/objects/typing.tsv: -------------------------------------------------------------------------------- 1 | plasmid type 2 | reference community_0_subcommunity_0 3 | reverse community_0_subcommunity_0 4 | 3_dup community_0_subcommunity_0 5 | 2_dup_3_dup community_0_subcommunity_0 6 | 3_dup_w_inverse community_0_subcommunity_0 7 | outlier community_1_subcommunity_0 8 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | Communities visualisation 6 | 7 | 8 | 9 | 10 |

Communities visualisation

11 | 12 | View community_0 (5 nodes, 10 edges)
13 | View community_1 (1 nodes, 0 edges)
14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_444444_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_555555_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_555555_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777620_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777620_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777777_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_777777_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_cc0000_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_cc0000_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_ffffff_256x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/communities/libs/resources/images/ui-icons_ffffff_256x240.png -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/subcommunities/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | subcommunity visualisation 6 | 7 | 8 | 9 | 10 |

subcommunity visualisation

11 | 12 | View community_0_subcommunity_0 (5 nodes, 10 edges)
13 | View community_1_subcommunity_0 (1 nodes, 0 edges)
14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/busy.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/busy.gif -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_1/truth/skip/dcj_thresh_4_graph/visualisations/subcommunities/libs/resources/images/ui-icons_444444_256x240.png: -------------------------------------------------------------------------------- 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3_dup_w_inverse 3_dup 1 11 | 3_dup_w_inverse 2_dup_3_dup 2 12 | del_rearrange reference_2 3 13 | inversion reference_2 1 14 | inversion del_rearrange 3 15 | dup_and_inverse reference_2 2 16 | dup_and_inverse del_rearrange 3 17 | dup_and_inverse inversion 1 18 | inverse_block reference_2 1 19 | inverse_block del_rearrange 3 20 | inverse_block inversion 0 21 | inverse_block dup_and_inverse 1 22 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/.snakemake_timestamp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/.snakemake_timestamp -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_0.txt: -------------------------------------------------------------------------------- 1 | ['reverse', 'reference'] 2 | ['3_dup', 'reference'] 3 | ['3_dup', 'reverse'] 4 | ['outlier', 'reference'] 5 | ['outlier', 'reverse'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_1.txt: -------------------------------------------------------------------------------- 1 | ['outlier', '3_dup'] 2 | ['2_dup_3_dup', 'reference'] 3 | ['2_dup_3_dup', 'reverse'] 4 | ['2_dup_3_dup', '3_dup'] 5 | ['2_dup_3_dup', 'outlier'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_10.txt: -------------------------------------------------------------------------------- 1 | ['inverse_block', '3_dup_w_inverse'] 2 | ['inverse_block', 'reference_2'] 3 | ['inverse_block', 'del_rearrange'] 4 | ['inverse_block', 'inversion'] 5 | ['inverse_block', 'dup_and_inverse'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_2.txt: -------------------------------------------------------------------------------- 1 | ['3_dup_w_inverse', 'reference'] 2 | ['3_dup_w_inverse', 'reverse'] 3 | ['3_dup_w_inverse', '3_dup'] 4 | ['3_dup_w_inverse', 'outlier'] 5 | ['3_dup_w_inverse', '2_dup_3_dup'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_3.txt: -------------------------------------------------------------------------------- 1 | ['reference_2', 'reference'] 2 | ['reference_2', 'reverse'] 3 | ['reference_2', '3_dup'] 4 | ['reference_2', 'outlier'] 5 | ['reference_2', '2_dup_3_dup'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_4.txt: -------------------------------------------------------------------------------- 1 | ['reference_2', '3_dup_w_inverse'] 2 | ['del_rearrange', 'reference'] 3 | ['del_rearrange', 'reverse'] 4 | ['del_rearrange', '3_dup'] 5 | ['del_rearrange', 'outlier'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_5.txt: -------------------------------------------------------------------------------- 1 | ['del_rearrange', '2_dup_3_dup'] 2 | ['del_rearrange', '3_dup_w_inverse'] 3 | ['del_rearrange', 'reference_2'] 4 | ['inversion', 'reference'] 5 | ['inversion', 'reverse'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_6.txt: -------------------------------------------------------------------------------- 1 | ['inversion', '3_dup'] 2 | ['inversion', 'outlier'] 3 | ['inversion', '2_dup_3_dup'] 4 | ['inversion', '3_dup_w_inverse'] 5 | ['inversion', 'reference_2'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_7.txt: -------------------------------------------------------------------------------- 1 | ['inversion', 'del_rearrange'] 2 | ['dup_and_inverse', 'reference'] 3 | ['dup_and_inverse', 'reverse'] 4 | ['dup_and_inverse', '3_dup'] 5 | ['dup_and_inverse', 'outlier'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_8.txt: -------------------------------------------------------------------------------- 1 | ['dup_and_inverse', '2_dup_3_dup'] 2 | ['dup_and_inverse', '3_dup_w_inverse'] 3 | ['dup_and_inverse', 'reference_2'] 4 | ['dup_and_inverse', 'del_rearrange'] 5 | ['dup_and_inverse', 'inversion'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batch_9.txt: -------------------------------------------------------------------------------- 1 | ['inverse_block', 'reference'] 2 | ['inverse_block', 'reverse'] 3 | ['inverse_block', '3_dup'] 4 | ['inverse_block', 'outlier'] 5 | ['inverse_block', '2_dup_3_dup'] -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/batches/batching_info.txt: -------------------------------------------------------------------------------- 1 | 5 2 | 11 -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/containment/all_pairs_containment_distance.tsv: -------------------------------------------------------------------------------- 1 | plasmid_1 plasmid_2 distance 2 | reverse reference 0.0 3 | 3_dup reference 0.0 4 | 3_dup reverse 0.0 5 | outlier reference 1.0 6 | outlier reverse 1.0 7 | outlier 3_dup 1.0 8 | 2_dup_3_dup reference 0.0 9 | 2_dup_3_dup reverse 0.0 10 | 2_dup_3_dup 3_dup 0.0 11 | 2_dup_3_dup outlier 1.0 12 | 3_dup_w_inverse reference 0.004930966469428033 13 | 3_dup_w_inverse reverse 0.004930966469428033 14 | 3_dup_w_inverse 3_dup 0.0 15 | 3_dup_w_inverse outlier 1.0 16 | 3_dup_w_inverse 2_dup_3_dup 0.0 17 | reference_2 reference 0.21055226824457596 18 | reference_2 reverse 0.21055226824457596 19 | reference_2 3_dup 0.45221843003412965 20 | reference_2 outlier 1.0 21 | reference_2 2_dup_3_dup 0.5258493353028064 22 | reference_2 3_dup_w_inverse 0.4621160409556314 23 | del_rearrange reference 0.717948717948718 24 | del_rearrange reverse 0.717948717948718 25 | del_rearrange 3_dup 0.8047781569965871 26 | del_rearrange outlier 1.0 27 | del_rearrange 2_dup_3_dup 0.819330385344283 28 | del_rearrange 3_dup_w_inverse 0.8081911262798634 29 | del_rearrange reference_2 0.0 30 | inversion reference 0.21055226824457596 31 | inversion reverse 0.21055226824457596 32 | inversion 3_dup 0.45358361774744027 33 | inversion outlier 1.0 34 | inversion 2_dup_3_dup 0.5270310192023634 35 | inversion 3_dup_w_inverse 0.4621160409556314 36 | inversion reference_2 0.002399808015358773 37 | inversion del_rearrange 0.006317119393556503 38 | dup_and_inverse reference 0.21055226824457596 39 | dup_and_inverse reverse 0.21055226824457596 40 | dup_and_inverse 3_dup 0.45358361774744027 41 | dup_and_inverse outlier 1.0 42 | dup_and_inverse 2_dup_3_dup 0.5270310192023634 43 | dup_and_inverse 3_dup_w_inverse 0.4621160409556314 44 | dup_and_inverse reference_2 0.004799616030717546 45 | dup_and_inverse del_rearrange 0.006317119393556503 46 | dup_and_inverse inversion 0.0 47 | inverse_block reference 0.21055226824457596 48 | inverse_block reverse 0.21055226824457596 49 | inverse_block 3_dup 0.45358361774744027 50 | inverse_block outlier 1.0 51 | inverse_block 2_dup_3_dup 0.5270310192023634 52 | inverse_block 3_dup_w_inverse 0.4621160409556314 53 | inverse_block reference_2 0.0 54 | inverse_block del_rearrange 0.006317119393556503 55 | inverse_block inversion 0.002399808015358773 56 | inverse_block dup_and_inverse 0.0 57 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/containment/containment_communities/objects/communities.tsv: -------------------------------------------------------------------------------- 1 | plasmid community 2 | 2_dup_3_dup community_0 3 | reverse community_0 4 | 3_dup_w_inverse community_0 5 | reference community_0 6 | 3_dup community_0 7 | inversion community_1 8 | del_rearrange community_1 9 | inverse_block community_1 10 | reference_2 community_1 11 | dup_and_inverse community_1 12 | outlier community_2 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/containment/containment_communities/objects/communities.txt: -------------------------------------------------------------------------------- 1 | 2_dup_3_dup reverse 3_dup_w_inverse reference 3_dup 2 | inversion del_rearrange inverse_block reference_2 dup_and_inverse 3 | outlier 4 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/dcj_thresh_4_graph/objects/hub_plasmids.csv: -------------------------------------------------------------------------------- 1 | hub_plasmids 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/dcj_thresh_4_graph/objects/typing.tsv: -------------------------------------------------------------------------------- 1 | plasmid type 2 | 2_dup_3_dup community_0_subcommunity_0 3 | reverse community_0_subcommunity_0 4 | 3_dup_w_inverse community_0_subcommunity_0 5 | reference community_0_subcommunity_0 6 | 3_dup community_0_subcommunity_0 7 | inversion community_1_subcommunity_0 8 | del_rearrange community_1_subcommunity_0 9 | inverse_block community_1_subcommunity_0 10 | reference_2 community_1_subcommunity_0 11 | dup_and_inverse community_1_subcommunity_0 12 | outlier community_2_subcommunity_0 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_0_align.unimog: -------------------------------------------------------------------------------- 1 | >reverse~reference:reverse 2 | 1 ) 3 | >reverse~reference:reference 4 | -1 ) 5 | >3_dup~reference:3_dup 6 | 1 2 ) 7 | >3_dup~reference:reference 8 | 1 ) 9 | >3_dup~reverse:3_dup 10 | 1 2 ) 11 | >3_dup~reverse:reverse 12 | -1 ) 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_0_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | reverse~reference reverse 1 1 2029 3 | reference -1 1 2029 4 | 3_dup~reference 3_dup 1 1 2029 5 | 3_dup 2 2029 2931 6 | reference 1 1 2029 7 | 3_dup~reverse 3_dup 1 1 2029 8 | 3_dup 2 2029 2931 9 | reverse -1 1 2029 10 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_10_align.unimog: -------------------------------------------------------------------------------- 1 | >inverse_block~reference_2:inverse_block 2 | 1 2 ) 3 | >inverse_block~reference_2:reference_2 4 | 1 -2 ) 5 | >inverse_block~del_rearrange:inverse_block 6 | 1 4 2 3 ) 7 | >inverse_block~del_rearrange:del_rearrange 8 | -3 1 -2 ) 9 | >inverse_block~inversion:inverse_block 10 | 1 2 ) 11 | >inverse_block~inversion:inversion 12 | -1 -2 ) 13 | >inverse_block~dup_and_inverse:inverse_block 14 | 1 2 ) 15 | >inverse_block~dup_and_inverse:dup_and_inverse 16 | -1 3 -2 ) 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_10_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | inverse_block~reference_2 inverse_block 1 1 1554 3 | inverse_block 2 1574 4148 4 | reference_2 1 1 1554 5 | reference_2 -2 1574 4148 6 | inverse_block~del_rearrange inverse_block 1 1 550 7 | inverse_block 4 550 1574 8 | inverse_block 2 1574 1784 9 | inverse_block 3 1807 4148 10 | del_rearrange -3 1 2342 11 | del_rearrange 1 2365 2914 12 | del_rearrange -2 2937 3147 13 | inverse_block~inversion inverse_block 1 1 1574 14 | inverse_block 2 1574 4158 15 | inversion -1 1 1574 16 | inversion -2 1584 4168 17 | inverse_block~dup_and_inverse inverse_block 1 1 1574 18 | inverse_block 2 1574 4168 19 | dup_and_inverse -1 1 1574 20 | dup_and_inverse 3 1574 3938 21 | dup_and_inverse -2 3938 6532 22 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_1_align.unimog: -------------------------------------------------------------------------------- 1 | >2_dup_3_dup~reference:2_dup_3_dup 2 | 1 2 2 3 4 ) 3 | >2_dup_3_dup~reference:reference 4 | 1 2 3 ) 5 | >2_dup_3_dup~reverse:2_dup_3_dup 6 | 1 2 2 3 4 ) 7 | >2_dup_3_dup~reverse:reverse 8 | -3 -2 -1 ) 9 | >2_dup_3_dup~3_dup:2_dup_3_dup 10 | 1 2 2 3 ) 11 | >2_dup_3_dup~3_dup:3_dup 12 | 1 2 3 ) 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_1_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 2_dup_3_dup~reference 2_dup_3_dup 1 1 550 3 | 2_dup_3_dup 2 578 1005 4 | 2_dup_3_dup 2 1033 1460 5 | 2_dup_3_dup 3 1488 2484 6 | 2_dup_3_dup 4 2484 3386 7 | reference 1 1 550 8 | reference 2 578 1005 9 | reference 3 1033 2029 10 | 2_dup_3_dup~reverse 2_dup_3_dup 1 1 550 11 | 2_dup_3_dup 2 578 1005 12 | 2_dup_3_dup 2 1033 1460 13 | 2_dup_3_dup 3 1488 2484 14 | 2_dup_3_dup 4 2484 3386 15 | reverse -3 1 997 16 | reverse -2 1025 1452 17 | reverse -1 1480 2029 18 | 2_dup_3_dup~3_dup 2_dup_3_dup 1 1 550 19 | 2_dup_3_dup 2 578 1005 20 | 2_dup_3_dup 2 1033 1460 21 | 2_dup_3_dup 3 1488 3386 22 | 3_dup 1 1 550 23 | 3_dup 2 578 1005 24 | 3_dup 3 1033 2931 25 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_2_align.unimog: -------------------------------------------------------------------------------- 1 | >3_dup_w_inverse~reference:3_dup_w_inverse 2 | 1 2 3 ) 3 | >3_dup_w_inverse~reference:reference 4 | 1 -2 ) 5 | >3_dup_w_inverse~reverse:3_dup_w_inverse 6 | 1 2 3 ) 7 | >3_dup_w_inverse~reverse:reverse 8 | 2 -1 ) 9 | >3_dup_w_inverse~3_dup:3_dup_w_inverse 10 | 1 2 3 ) 11 | >3_dup_w_inverse~3_dup:3_dup 12 | 1 -2 3 ) 13 | >3_dup_w_inverse~2_dup_3_dup:3_dup_w_inverse 14 | 1 2 3 ) 15 | >3_dup_w_inverse~2_dup_3_dup:2_dup_3_dup 16 | 1 4 -2 3 ) 17 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_2_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | 3_dup_w_inverse~reference 3_dup_w_inverse 1 1 563 3 | 3_dup_w_inverse 2 563 2019 4 | 3_dup_w_inverse 3 2019 2931 5 | reference 1 1 563 6 | reference -2 563 2019 7 | 3_dup_w_inverse~reverse 3_dup_w_inverse 1 1 563 8 | 3_dup_w_inverse 2 563 2019 9 | 3_dup_w_inverse 3 2019 2931 10 | reverse 2 11 1467 11 | reverse -1 1467 2029 12 | 3_dup_w_inverse~3_dup 3_dup_w_inverse 1 1 563 13 | 3_dup_w_inverse 2 563 2019 14 | 3_dup_w_inverse 3 2019 2931 15 | 3_dup 1 1 563 16 | 3_dup -2 563 2019 17 | 3_dup 3 2019 2931 18 | 3_dup_w_inverse~2_dup_3_dup 3_dup_w_inverse 1 1 563 19 | 3_dup_w_inverse 2 563 2019 20 | 3_dup_w_inverse 3 2019 2931 21 | 2_dup_3_dup 1 1 563 22 | 2_dup_3_dup 4 563 1018 23 | 2_dup_3_dup -2 1018 2474 24 | 2_dup_3_dup 3 2474 3386 25 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_3_align.unimog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_3_align.unimog -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_3_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_4_align.unimog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_4_align.unimog -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_4_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_5_align.unimog: -------------------------------------------------------------------------------- 1 | >del_rearrange~reference_2:del_rearrange 2 | 1 2 3 ) 3 | >del_rearrange~reference_2:reference_2 4 | 2 4 1 3 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_5_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | del_rearrange~reference_2 del_rearrange 1 1 2342 3 | del_rearrange 2 2365 2914 4 | del_rearrange 3 2937 3167 5 | reference_2 2 1 550 6 | reference_2 4 550 1574 7 | reference_2 1 1574 3915 8 | reference_2 3 3938 4168 9 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_6_align.unimog: -------------------------------------------------------------------------------- 1 | >inversion~reference_2:inversion 2 | 1 2 ) 3 | >inversion~reference_2:reference_2 4 | -1 2 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_6_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | inversion~reference_2 inversion 1 11 1574 3 | inversion 2 1594 4168 4 | reference_2 -1 1 1564 5 | reference_2 2 1574 4148 6 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_7_align.unimog: -------------------------------------------------------------------------------- 1 | >inversion~del_rearrange:inversion 2 | 4 1 2 3 ) 3 | >inversion~del_rearrange:del_rearrange 4 | 2 -1 3 ) 5 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_7_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | inversion~del_rearrange inversion 4 1 1025 3 | inversion 1 1025 1574 4 | inversion 2 1594 3935 5 | inversion 3 3958 4168 6 | del_rearrange 2 1 2342 7 | del_rearrange -1 2365 2914 8 | del_rearrange 3 2937 3147 9 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_8_align.unimog: -------------------------------------------------------------------------------- 1 | >dup_and_inverse~reference_2:dup_and_inverse 2 | 1 3 2 ) 3 | >dup_and_inverse~reference_2:reference_2 4 | -1 2 ) 5 | >dup_and_inverse~del_rearrange:dup_and_inverse 6 | 4 1 2 5 3 ) 7 | >dup_and_inverse~del_rearrange:del_rearrange 8 | 2 -1 3 ) 9 | >dup_and_inverse~inversion:dup_and_inverse 10 | 1 2 2 3 ) 11 | >dup_and_inverse~inversion:inversion 12 | 1 2 3 ) 13 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_8_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | dup_and_inverse~reference_2 dup_and_inverse 1 24 1574 3 | dup_and_inverse 3 1574 3958 4 | dup_and_inverse 2 3958 6532 5 | reference_2 -1 1 1551 6 | reference_2 2 1574 4148 7 | dup_and_inverse~del_rearrange dup_and_inverse 4 1 1025 8 | dup_and_inverse 1 1025 1571 9 | dup_and_inverse 2 1594 3948 10 | dup_and_inverse 5 3948 6322 11 | dup_and_inverse 3 6322 6532 12 | del_rearrange 2 1 2355 13 | del_rearrange -1 2368 2914 14 | del_rearrange 3 2937 3147 15 | dup_and_inverse~inversion dup_and_inverse 1 1 1584 16 | dup_and_inverse 2 1594 3948 17 | dup_and_inverse 2 3958 6312 18 | dup_and_inverse 3 6322 6532 19 | inversion 1 1 1584 20 | inversion 2 1594 3948 21 | inversion 3 3958 4168 22 | -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_9_align.unimog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/pling/4b07ff44660cce8d446d7f8fded9f43ce16f6e35/tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_9_align.unimog -------------------------------------------------------------------------------- /tests/unimog_tests/test_cases/toy_tests/test_2/truth/align/unimogs/batch_9_map.txt: -------------------------------------------------------------------------------- 1 | Plasmid Block_ID Start End 2 | -------------------------------------------------------------------------------- /tests/utils.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | 3 | # Instance of the TestCase to use the assertEqual method 4 | tc = unittest.TestCase() 5 | 6 | 7 | def read_file(path): 8 | """Helper method to read a file.""" 9 | with open(path, 'rb') as f: 10 | return f.read() 11 | 12 | 13 | def assert_files_are_identical(path_to_first_file, path_to_second_file): 14 | first_file_content = read_file(path_to_first_file) 15 | second_file_content = read_file(path_to_second_file) 16 | tc.assertEqual(first_file_content, second_file_content) 17 | 18 | def get_num_communities(filepath): 19 | with open(filepath) as communities_fh: 20 | num = len(communities_fh.readlines()) 21 | return num 22 | 23 | def get_batch_num(filepath): 24 | with open(filepath) as f: 25 | next(f) 26 | num = int(f.readline().strip()) 27 | return num 28 | 29 | def assert_containment(test, test_dir, integerisation): 30 | assert_files_are_identical(f"{test_dir}/{test}/out/{integerisation}/containment/all_pairs_containment_distance.tsv", 31 | f"{test_dir}/{test}/truth/{integerisation}/containment/all_pairs_containment_distance.tsv") 32 | assert_files_are_identical(f"{test_dir}/{test}/out/{integerisation}/containment/containment_communities/objects/communities.tsv", 33 | f"{test_dir}/{test}/truth/{integerisation}/containment/containment_communities/objects/communities.tsv") 34 | assert_files_are_identical(f"{test_dir}/{test}/out/{integerisation}/containment/containment_communities/objects/communities.txt", 35 | f"{test_dir}/{test}/truth/{integerisation}/containment/containment_communities/objects/communities.txt") 36 | 37 | def assert_align_unimogs(test, test_dir, batch_num): 38 | for i in range(batch_num): 39 | assert_files_are_identical(f"{test_dir}/{test}/out/align/unimogs/batch_{i}_align.unimog", 40 | f"{test_dir}/{test}/truth/align/unimogs/batch_{i}_align.unimog") 41 | assert_files_are_identical(f"{test_dir}/{test}/out/align/unimogs/batch_{i}_map.txt", 42 | f"{test_dir}/{test}/truth/align/unimogs/batch_{i}_map.txt") 43 | 44 | def assert_end_to_end(test, dir): 45 | #containment communities 46 | assert_containment(test, dir, "align") 47 | #unimogs 48 | batch_num = get_batch_num(f"{dir}/{test}/out/align/batches/batching_info.txt") 49 | assert_align_unimogs(test, dir, batch_num) 50 | #DCJ distance matrix 51 | assert_files_are_identical(f"{dir}/{test}/out/align/all_plasmids_distances.tsv", 52 | f"{dir}/{test}/truth/align/all_plasmids_distances.tsv") 53 | #DCJ communities 54 | assert_files_are_identical(f"{dir}/{test}/out/align/dcj_thresh_4_graph/objects/typing.tsv", 55 | f"{dir}/{test}/truth/align/dcj_thresh_4_graph/objects/typing.tsv") 56 | assert_files_are_identical(f"{dir}/{test}/out/align/dcj_thresh_4_graph/objects/hub_plasmids.csv", 57 | f"{dir}/{test}/truth/align/dcj_thresh_4_graph/objects/hub_plasmids.csv") 58 | --------------------------------------------------------------------------------