├── .bumpversion.cfg ├── .coveragerc ├── .gitattributes ├── .github └── workflows │ ├── codeql-analysis.yml │ ├── publish-to-test-pypi.yml │ └── python-package.yml ├── .gitignore ├── AUTHORS ├── CHANGELOG.md ├── DESCRIPTION.md ├── Daijin_tutorial.spombe.rst ├── Docker └── Dockerfile.ubuntu ├── LICENSE.txt ├── MANIFEST.in ├── Mikado.dot ├── Mikado.srctrlbm ├── Mikado.srctrldb ├── Mikado.srctrlprj ├── Mikado ├── __init__.py ├── __main__.py ├── _transcripts │ ├── __init__.py │ ├── clique_methods.py │ ├── scoring_configuration.py │ ├── transcript_base.py │ └── transcript_methods │ │ ├── __init__.py │ │ ├── finalizing.py │ │ └── printing.py ├── configuration │ ├── __init__.py │ ├── configuration.py │ ├── configurator.py │ ├── daijin_configuration.py │ ├── daijin_configurator.py │ ├── picking_config.py │ ├── prepare_config.py │ ├── scoring_files │ │ ├── HISTORIC │ │ │ ├── athaliana_scoring.yaml │ │ │ ├── celegans_scoring.yaml │ │ │ ├── dmelanogaster_scoring.yaml │ │ │ ├── hsapiens_scoring.yaml │ │ │ ├── human.yaml │ │ │ ├── insects.yaml │ │ │ ├── mammalian.yaml │ │ │ ├── plant.yaml │ │ │ ├── plants.yaml │ │ │ ├── scerevisiae.yaml │ │ │ └── worm.yaml │ │ ├── mammalian.yaml │ │ └── plant.yaml │ └── serialise_config.py ├── daijin │ ├── .gitignore │ ├── __init__.py │ ├── __main__.py │ ├── assemble.py │ ├── assemble.smk │ ├── envs │ │ ├── blast.yaml │ │ ├── cufflinks.yaml │ │ ├── diamond.yaml │ │ ├── gmap.yaml │ │ ├── gnuplot.yaml │ │ ├── hisat2.yaml │ │ ├── portcullis.yaml │ │ ├── prodigal.yaml │ │ ├── samtools.yaml │ │ ├── scallop.yaml │ │ ├── star.yaml │ │ ├── stringtie.yaml │ │ ├── tophat2.yaml │ │ ├── transdecoder.yaml │ │ └── trinity.yaml │ ├── hpc.yaml │ ├── mikado.py │ └── mikado.smk ├── exceptions.py ├── loci │ ├── __init__.py │ ├── abstractlocus.py │ ├── excluded.py │ ├── locus.py │ ├── monosublocus.py │ ├── monosublocusholder.py │ ├── sublocus.py │ └── superlocus.py ├── parsers │ ├── GFF.py │ ├── GTF.py │ ├── __init__.py │ ├── bam_parser.py │ ├── bed12.py │ ├── blast_utils.py │ ├── gfannotation.py │ └── parser.py ├── picking │ ├── __init__.py │ ├── _loci_serialiser.py │ ├── _locus_line_creator.py │ ├── _locus_single_printer.py │ ├── _merge_loci_utils.py │ ├── loci_processer.py │ └── picker.py ├── preparation │ ├── __init__.py │ ├── annotation_parser.py │ ├── checking.py │ └── prepare.py ├── scales │ ├── __init__.py │ ├── accountant.py │ ├── assignment │ │ ├── __init__.py │ │ ├── assigner.py │ │ └── distributed.py │ ├── calculator.py │ ├── class_codes.py │ ├── compare.py │ ├── contrast.pxd │ ├── contrast.pyx │ ├── prediction_parsers │ │ ├── __init__.py │ │ ├── parse_bam_prediction.py │ │ ├── parse_bed12.py │ │ ├── parse_gff3_prediction.py │ │ ├── parse_gtf_prediction.py │ │ └── transmission.py │ ├── reference_preparation │ │ ├── __init__.py │ │ ├── gene_dict.py │ │ ├── indexing.py │ │ └── prepare_reference.py │ └── resultstorer.py ├── serializers │ ├── __init__.py │ ├── blast_serializer │ │ ├── __init__.py │ │ ├── aln_string_parser.pyx │ │ ├── blast_serialiser.py │ │ ├── btop_parser.pxd │ │ ├── btop_parser.pyx │ │ ├── hit.py │ │ ├── hsp.py │ │ ├── query.py │ │ ├── tab_serialiser.py │ │ ├── tabular_utils.py │ │ ├── target.py │ │ ├── utils.py │ │ ├── xml_serialiser.py │ │ └── xml_utils.py │ ├── external.py │ ├── junction.py │ └── orf.py ├── subprograms │ ├── __init__.py │ ├── __main__.py │ ├── _utils.py │ ├── compare.py │ ├── configure.py │ ├── pick.py │ ├── prepare.py │ ├── serialise.py │ └── util │ │ ├── __init__.py │ │ ├── awk_gtf.py │ │ ├── class_codes.py │ │ ├── collapse_compare_stats.py │ │ ├── convert.py │ │ ├── grep.py │ │ ├── metrics.py │ │ ├── stats.py │ │ └── trim.py ├── tests │ ├── Chrysemys_picta_bellii_problematic.gff3 │ ├── Chrysemys_picta_bellii_problematic.list.txt │ ├── Chrysemys_picta_bellii_problematic.txt │ ├── ERR588038.R1.fq.gz │ ├── ERR588038.R2.fq.gz │ ├── NC_037283.1.fa.gz │ ├── SRR5037293.pacbio.fastq.gz │ ├── __init__.py │ ├── annotation.gff3 │ ├── annotation.gff3.stats │ ├── assigner_test.py │ ├── blast_data │ │ ├── diamond.0.9.30.tsv.gz │ │ ├── diamond.0.9.30.xml.gz │ │ ├── transcripts.fasta │ │ └── transcripts.fasta.fai │ ├── blast_input_tests │ │ ├── commands.sh │ │ ├── queries.fasta │ │ ├── queries.fasta.fai │ │ ├── sanitised │ │ │ ├── blast │ │ │ │ ├── tsv │ │ │ │ │ └── blast.tsv.gz │ │ │ │ └── xml │ │ │ │ │ └── blast.xml.gz │ │ │ ├── blast_parse_seqids │ │ │ │ ├── tsv │ │ │ │ │ └── blast.tsv.gz │ │ │ │ └── xml │ │ │ │ │ └── blast.xml.gz │ │ │ ├── diamond │ │ │ │ ├── daa │ │ │ │ │ └── blast.daa │ │ │ │ ├── tsv │ │ │ │ │ └── blast.tsv.gz │ │ │ │ └── xml │ │ │ │ │ └── blast.xml.gz │ │ │ ├── uniprot.fasta │ │ │ └── uniprot.fasta.fai │ │ ├── uniprot.fasta │ │ └── uniprot │ │ │ ├── blast │ │ │ ├── tsv │ │ │ │ └── blast.tsv.gz │ │ │ └── xml │ │ │ │ └── blast.xml.gz │ │ │ ├── blast_parse_seqids │ │ │ ├── tsv │ │ │ │ └── blast.tsv.gz │ │ │ └── xml │ │ │ │ └── blast.xml.gz │ │ │ ├── diamond │ │ │ ├── daa │ │ │ │ └── blast.daa │ │ │ ├── tsv │ │ │ │ └── blast.tsv.gz │ │ │ └── xml │ │ │ │ └── blast.xml.gz │ │ │ ├── uniprot.fasta │ │ │ └── uniprot.fasta.fai │ ├── cds_test_1.gtf │ ├── cds_test_2.gtf │ ├── check_seed.fa │ ├── check_seed.gtf │ ├── check_seed.yaml │ ├── chr5.fas.gz │ ├── chr5.fas.gz.fai │ ├── chr5.fas.gz.gzi │ ├── chunk-001-proteins.xml.gz │ ├── complete_padding.bed12 │ ├── configuration.yaml │ ├── cufflinks.gtf │ ├── cufflinks.no_transcript.gtf │ ├── external.yaml │ ├── fusion_test │ │ ├── fusion_test_pred.gtf │ │ └── fusion_test_ref.gff3 │ ├── genome.fai │ ├── gtf_check.gtf.gz │ ├── intervaltree_test.py │ ├── junctions.bed │ ├── junctions_duplicates.bed │ ├── locus_test.py │ ├── mikado.blast.asn.gz │ ├── mikado.blast.xml │ ├── mikado.db │ ├── mikado_prepared.fasta │ ├── mikado_prepared.fasta.fai │ ├── mikado_prepared.gtf │ ├── neg_pad.bed12 │ ├── neg_pad.fa │ ├── neg_pad.fa.fai │ ├── orf_test.py │ ├── pacbio.bam │ ├── pad_three_neg.bed12 │ ├── pad_utr.bed12 │ ├── padding_test.bed12 │ ├── padding_test.fa │ ├── padding_test.fa.fai │ ├── padding_test.rev_compl.bed12 │ ├── padding_test.rev_compl.fa │ ├── padding_test.rev_compl.fa.fai │ ├── parser_test.py │ ├── phasing_padding.bed12 │ ├── plants.suspicious_requirement.yaml │ ├── prepare_misc_test.py │ ├── reference.gff3 │ ├── scoring_only_cds.yaml │ ├── test.reads.bam │ ├── test_bed12.py │ ├── test_blast_inputs.py │ ├── test_blast_related.py │ ├── test_clique_methods.py │ ├── test_compare.py │ ├── test_configurators.py │ ├── test_db_utils.py │ ├── test_external │ │ ├── abundance.h5 │ │ ├── abundance.tsv │ │ ├── data.txt │ │ ├── mikado_prepared.fasta │ │ ├── mikado_prepared.fasta.fai │ │ ├── wrong_1.tsv │ │ └── wrong_2.tsv │ ├── test_external_aphid │ │ ├── annotation_run1.metrics.testds.txt │ │ ├── aphid.scoring.yaml │ │ ├── mikado.configuration.testds.yaml │ │ ├── mikado_prepared.testds.fasta │ │ └── mikado_prepared.testds.fasta.fai │ ├── test_external_async.py │ ├── test_external_scores.py │ ├── test_gene.py │ ├── test_invalid_orfs.py │ ├── test_light.py │ ├── test_mRNA.bam │ ├── test_mRNA.bam.bai │ ├── test_metrics.py │ ├── test_modifications.py │ ├── test_scores.py │ ├── test_serialise_external.py │ ├── test_serialise_junctions.py │ ├── test_splitting.py │ ├── test_system_calls.py │ ├── test_transcript_checker.py │ ├── test_transcript_methods.py │ ├── test_transcript_negative.py │ ├── test_transcript_positive.py │ ├── test_transcript_single.py │ ├── test_truncated_cds.fa │ ├── test_truncated_cds.fa.fai │ ├── test_truncated_cds.gff3 │ ├── test_utils.py │ ├── transcripts.fasta.prodigal.gff3 │ ├── trinity.bam │ ├── trinity.bed12 │ ├── trinity.cDNA_match.gff3 │ ├── trinity.gff3 │ ├── trinity.gtf │ ├── trinity.ids │ ├── trinity.match_matchpart.gff3 │ ├── trinity.minimap2.bam │ ├── trinity.minimap2.bam.bai │ ├── trinity.no_transcript_feature.gtf │ ├── trinity_stats.txt │ ├── trinity_unsorted.gff3 │ ├── trinity_unsorted.gtf │ ├── uniprot_sprot_plants.fasta.gz │ ├── uniprot_sprot_plants.fasta.gz.fai │ ├── uniprot_sprot_plants.fasta.gz.gzi │ ├── utilities_test.py │ └── zom_junctions.bed ├── transcripts │ ├── __init__.py │ ├── pad.py │ ├── reference_gene.py │ ├── transcript.py │ ├── transcript_methods │ │ ├── __init__.py │ │ ├── retrieval.py │ │ └── splitting.py │ ├── transcriptchecker.py │ └── transcriptcomputer.py ├── utilities │ ├── __init__.py │ ├── dbutils.py │ ├── f1.pxd │ ├── f1.pyx │ ├── file_type.py │ ├── intervaltree.pxd │ ├── intervaltree.pyx │ ├── log_utils.py │ ├── namespace.py │ ├── overlap.pxd │ └── overlap.pyx └── version.py ├── README.md ├── Singularity ├── Singularity.centos.def ├── Singularity.conda.def └── Singularity.ubuntu.def ├── codecov.yaml ├── conda ├── build.sh └── meta.yaml ├── docs ├── Algorithms.rst ├── Installation.rst ├── Introduction.rst ├── Library │ ├── Mikado.configuration.rst │ ├── Mikado.daijin.rst │ ├── Mikado.loci.rst │ ├── Mikado.parsers.rst │ ├── Mikado.picking.rst │ ├── Mikado.preparation.rst │ ├── Mikado.rst │ ├── Mikado.scales.rst │ ├── Mikado.serializers.blast_serializer.rst │ ├── Mikado.serializers.rst │ ├── Mikado.subprograms.rst │ ├── Mikado.subprograms.util.rst │ ├── Mikado.transcripts.rst │ ├── Mikado.transcripts.transcript_methods.rst │ ├── Mikado.utilities.rst │ └── modules.rst ├── Makefile ├── Mikado_algorithm.jpeg ├── References.rst ├── Scoring_files.rst ├── Tutorial │ ├── Adapting.rst │ ├── Daijin_tutorial.rst │ ├── Scoring_tutorial.rst │ ├── Snakefile │ ├── assemble_pipeline.png │ ├── chr5.fas.gz │ ├── class.gtf │ ├── cufflinks.gtf │ ├── daijin.yaml │ ├── daijin_result.png │ ├── index.rst │ ├── junctions.bed │ ├── mikado.png │ ├── mikado_pipeline.png │ ├── orfs.bed │ ├── plant.yaml │ ├── reference.gff3 │ ├── snake.png │ ├── snakemake_dag.png │ ├── snakemake_dag.svg │ ├── stringtie.gtf │ ├── trinity.gff3 │ └── uniprot_sprot_plants.fasta.gz ├── Usage │ ├── Compare.rst │ ├── Configure.rst │ ├── Daijin.rst │ ├── Pick.rst │ ├── Prepare.rst │ ├── Serialise.rst │ ├── TAIR10.stats │ ├── Utilities.rst │ ├── assemble.smk │ ├── daijin_assemble.png │ ├── daijin_assemble.svg │ ├── daijin_mikado.png │ ├── daijin_mikado.svg │ ├── database_schema.eps │ ├── database_schema.png │ ├── database_schema.svg │ ├── hpc.yaml │ ├── index.rst │ └── mikado.smk ├── _static │ └── theme_overrides.css ├── assets │ ├── Mikado_GenomeScience2016.pdf │ ├── Mikado_GenomeScience2016_poster.pdf │ └── Mikado_paper_2018_giy093.pdf ├── conf.py ├── coverage_shield.svg ├── index.rst ├── locus_example.jpeg ├── mikado-header.jpg ├── mikado-logo.jpg └── mikado-logo.png ├── environment.yml ├── pyproject.toml ├── requirements.txt ├── sample_data ├── ERR588038.R1.fq.gz ├── ERR588038.R2.fq.gz ├── SRR5037293.pacbio.fastq.gz ├── Snakefile ├── chr5.fas.gz ├── chr5.fas.gz.gzi ├── class.gtf ├── cufflinks.gtf ├── gffread.yaml ├── junctions.bed ├── kallisto.yaml ├── list.txt ├── mikado.bed ├── mikado_prepared.conf_alias.gtf ├── pacbio.bam ├── pacbio.bam.bai ├── plant_external.yaml ├── reference.gff3 ├── samples.txt ├── stringtie.gtf ├── 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