├── .copier-answers.yml ├── .gitattributes ├── .github └── workflows │ ├── ci-dev.yaml │ ├── join-release.yaml │ ├── tag-release.yaml │ └── update-copyright-headers.yaml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── conda-recipe └── meta.yaml ├── install-prior-versions.md ├── logo.png ├── pyproject.toml └── rescript ├── __init__.py ├── _utilities.py ├── assets └── index.html ├── bv_brc.py ├── citations.bib ├── cross_validate.py ├── degap.py ├── dereplicate.py ├── edit_taxonomy.py ├── evaluate.py ├── extract_seq_segments.py ├── filter_length.py ├── get_data.py ├── get_eukaryome.py ├── get_gtdb.py ├── get_midori2.py ├── get_pr2.py ├── get_unite.py ├── merge.py ├── ncbi.py ├── ncbi_datasets.py ├── orient.py ├── parse_silva_taxonomy.py ├── plugin_setup.py ├── screenseq.py ├── subsample.py ├── tests ├── __init__.py ├── data │ ├── Human-Kneecap.fasta │ ├── bakers-yeast.fasta │ ├── bakers-yeast.tsv │ ├── cleanseq-test-1-rna.fasta │ ├── cleanseq-test-1.fasta │ ├── degap-test-alignment.fasta │ ├── derep-taxa-numericIDs.tsv │ ├── derep-taxa.tsv │ ├── derep-test-fungi.fasta │ ├── derep-test-fungi.tsv │ ├── derep-test-numericIDs.fasta │ ├── derep-test.fasta │ ├── escherichia_shigella_taxonomy.txt │ ├── eukaryome-parsed-seqs.fasta │ ├── eukaryome-parsed-taxa.tsv │ ├── eukaryome-seqs.fasta │ ├── full-length-query.fasta │ ├── gtdb-seqs-archaea.fasta │ ├── gtdb-seqs-bacteria.fasta │ ├── gtdb-seqs.fasta │ ├── gtdb-tax.tsv │ ├── gtdb-taxa-archaea.tsv │ ├── gtdb-taxa-bacteria.tsv │ ├── midori2-seqs.fasta │ ├── midori2-taxa.tsv │ ├── mixed-orientations-rc.fasta │ ├── mixed-orientations.fasta │ ├── ncbi-dataset │ │ └── ncbi_dataset │ │ │ └── data │ │ │ ├── GCA_000008865.2 │ │ │ ├── GCA_000008865.2_ASM886v2_genomic.fna │ │ │ ├── genomic.gff │ │ │ ├── protein.faa │ │ │ └── sequence_report.jsonl │ │ │ ├── assembly_data_report.jsonl │ │ │ └── dataset_catalog.json │ ├── ncbi-responses.pkl │ ├── ncbi-seqs-protein.fasta │ ├── ncbi-seqs.fasta │ ├── ncbi-taxa-protein.tsv │ ├── ncbi-taxa.tsv │ ├── ns-ncbi-taxa.tsv │ ├── paired_end_data │ │ ├── Human-Copycat_S2_L001_R1_001.fastq.gz │ │ ├── Human-Copycat_S2_L001_R2_001.fastq.gz │ │ ├── Human-Kneecap_S1_L001_R1_001.fastq.gz │ │ ├── Human-Kneecap_S1_L001_R2_001.fastq.gz │ │ ├── MANIFEST │ │ └── metadata.yml │ ├── paired_end_data_expected │ │ ├── Human-Copycat_S2_L001_R1_001.fastq.gz │ │ ├── Human-Copycat_S2_L001_R2_001.fastq.gz │ │ ├── Human-Kneecap_S1_L001_R1_001.fastq.gz │ │ ├── Human-Kneecap_S1_L001_R2_001.fastq.gz │ │ ├── MANIFEST │ │ └── metadata.yml │ ├── pr2-seqs.fasta │ ├── pr2-tax-formatted.tsv │ ├── pr2-tax.tsv │ ├── real-taxa-test.tsv │ ├── ref-segs.fasta │ ├── single_end_data │ │ ├── Human-Copycat_S2_L001_R1_001.fastq.gz │ │ ├── Human-Kneecap_S1_L001_R1_001.fastq.gz │ │ ├── MANIFEST │ │ └── metadata.yml │ ├── single_end_data_expected │ │ ├── Human-Copycat_S2_L001_R1_001.fastq.gz │ │ ├── Human-Kneecap_S1_L001_R1_001.fastq.gz │ │ ├── MANIFEST │ │ └── metadata.yml │ ├── small-silva-full-len-alignment.fasta │ ├── small-silva-v4-trim-keeplength-nokeepprimers.fasta │ ├── small-silva-v4-trim-keeplength.fasta │ ├── small-silva-v4-trim-no-keeplength.fasta │ ├── taxid_tree.tre │ ├── taxid_tree_missing_id.tre │ ├── taxmap_test_match_tree.txt │ ├── taxonomy-replacement-full-strings.txt │ ├── taxonomy-replacement-pass.txt │ ├── taxonomy-replacement-regex.txt │ ├── trim-test-alignment-fwd.fasta │ ├── trim-test-alignment-rev.fasta │ ├── trim-test-alignment-with-primers-mess.fasta │ ├── trim-test-alignment-with-primers.fasta │ ├── trim-test-alignment.fasta │ ├── trim-test-sequences-trimmed.fasta │ ├── trim-test-sequences.fasta │ ├── unitefile.tgz │ └── unitefile_no_dev.tgz ├── test_bv_brc.py ├── test_cross_validate.py ├── test_degap.py ├── test_derep.py ├── test_edit_taxonomy.py ├── test_evaluate.py ├── test_extract_seq_segments.py ├── test_filter_length.py ├── test_get_data.py ├── test_get_eukaryome.py ├── test_get_gtdb.py ├── test_get_midori2.py ├── test_get_pr2.py ├── test_get_unite.py ├── test_merge.py ├── test_ncbi.py ├── test_ncbi_datasets.py ├── test_orient.py ├── test_parse_silva_taxonomy.py ├── test_screenseq.py ├── test_subsample.py └── test_trim_alignment.py ├── trim_alignment.py └── types ├── __init__.py ├── _format.py ├── _transformer.py ├── _type.py ├── methods.py └── tests ├── __init__.py ├── data ├── derep-test-rna.fasta ├── dna-with-gaps.fasta ├── empty.tsv ├── empty_with_header.tsv ├── rna-with-gaps.fasta ├── silva_taxa.tsv ├── silva_taxamap.tsv ├── silva_taxamap_v132.tsv └── trash_taxamap.tsv ├── test_methods.py └── test_types_formats_transformers.py /.copier-answers.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bokulich-lab/RESCRIPt/HEAD/.copier-answers.yml -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | 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