LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
q2_types_genomics/__init__.py
q2_types_genomics/_version.py
q2_types_genomics/citations.bib
q2_types_genomics/plugin_setup.py
q2_types_genomics.egg-info/PKG-INFO
q2_types_genomics.egg-info/SOURCES.txt
q2_types_genomics.egg-info/dependency_links.txt
q2_types_genomics.egg-info/entry_points.txt
q2_types_genomics.egg-info/not-zip-safe
q2_types_genomics.egg-info/top_level.txt
q2_types_genomics/feature_data/__init__.py
q2_types_genomics/feature_data/_format.py
q2_types_genomics/feature_data/_transformer.py
q2_types_genomics/feature_data/_type.py
q2_types_genomics/feature_data/tests/__init__.py
q2_types_genomics/feature_data/tests/test_format.py
q2_types_genomics/feature_data/tests/test_transformers.py
q2_types_genomics/feature_data/tests/test_type.py
q2_types_genomics/feature_data/tests/data/good_ortholog_annotation/test_output.emapper.annotations
q2_types_genomics/feature_data/tests/data/mags-fa/23c5b64e-3f3e-4688-9862-e9dae4fa0f5b.fa
q2_types_genomics/feature_data/tests/data/mags-fa/70c5a728-96a6-4eed-b9f9-9a73153c1385.fa
q2_types_genomics/feature_data/tests/data/mags-fa/7e2a749a-a19a-4b62-8195-0ee601b5fdfb.fa
q2_types_genomics/feature_data/tests/data/mags-fasta/3b7d53fb-5b60-46c6-8819-aeda065b12e9.fasta
q2_types_genomics/feature_data/tests/data/mags-fasta/6232c7e1-8ed7-47c8-9bdb-b94706a26931.fasta
q2_types_genomics/feature_data/tests/data/ortholog_annotation_extra/test_output.emapper.annotations
q2_types_genomics/feature_data/tests/data/ortholog_annotation_extra/test_output.emapper.orthologs
q2_types_genomics/feature_map/__init__.py
q2_types_genomics/feature_map/_format.py
q2_types_genomics/feature_map/_transformer.py
q2_types_genomics/feature_map/_type.py
q2_types_genomics/feature_map/tests/__init__.py
q2_types_genomics/feature_map/tests/test_format.py
q2_types_genomics/feature_map/tests/test_transformer.py
q2_types_genomics/feature_map/tests/test_type.py
q2_types_genomics/feature_map/tests/data/mag-to-contigs-empty-list.json
q2_types_genomics/feature_map/tests/data/mag-to-contigs-invalid-ids.json
q2_types_genomics/feature_map/tests/data/mag-to-contigs-invalid-values.json
q2_types_genomics/feature_map/tests/data/mag-to-contigs-valid.json
q2_types_genomics/genome_data/__init__.py
q2_types_genomics/genome_data/_format.py
q2_types_genomics/genome_data/_transformer.py
q2_types_genomics/genome_data/_type.py
q2_types_genomics/genome_data/tests/__init__.py
q2_types_genomics/genome_data/tests/test_format.py
q2_types_genomics/genome_data/tests/test_transformer.py
q2_types_genomics/genome_data/tests/test_type.py
q2_types_genomics/genome_data/tests/data/genes-with-prefix/ABC_123.1_genes.fa
q2_types_genomics/genome_data/tests/data/genes-with-prefix/BCD_234.2_genes.fa
q2_types_genomics/genome_data/tests/data/genes-with-suffix/genes1.fa
q2_types_genomics/genome_data/tests/data/genes-with-suffix/genes2.fa
q2_types_genomics/genome_data/tests/data/genes-with-wrong-prefix/wrongprefix1genes.fa
q2_types_genomics/genome_data/tests/data/genes-with-wrong-prefix/wrongprefix2genes.fa
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-corrupt.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-directive-empty.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-empty-feature.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-invalid-char.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-invalid-phase.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-invalid-start.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-invalid-strand.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-lines-unequal.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-negative-start.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-no-version.gff
q2_types_genomics/genome_data/tests/data/loci-invalid/loci-wrong-version.gff
q2_types_genomics/genome_data/tests/data/loci-with-prefix/ABC_123.1_loci.gff
q2_types_genomics/genome_data/tests/data/loci-with-prefix/BCD_234.2_loci.gff
q2_types_genomics/genome_data/tests/data/loci-with-suffix/loci1.gff
q2_types_genomics/genome_data/tests/data/loci-with-suffix/loci2.gff
q2_types_genomics/genome_data/tests/data/loci-with-wrong-prefix/wrongprefix1loci.gff
q2_types_genomics/genome_data/tests/data/loci-with-wrong-prefix/wrongprefix2loci.gff
q2_types_genomics/genome_data/tests/data/ortholog/test_sample.emapper.seed_orthologs
q2_types_genomics/genome_data/tests/data/proteins-with-prefix/ABC_123.1_proteins.faa
q2_types_genomics/genome_data/tests/data/proteins-with-prefix/BCD_234.2_proteins.faa
q2_types_genomics/genome_data/tests/data/proteins-with-suffix/proteins1.faa
q2_types_genomics/genome_data/tests/data/proteins-with-suffix/proteins2.faa
q2_types_genomics/genome_data/tests/data/proteins-with-wrong-prefix/wrongprefix1proteins.faa
q2_types_genomics/genome_data/tests/data/proteins-with-wrong-prefix/wrongprefix2proteins.faa
q2_types_genomics/kraken2/__init__.py
q2_types_genomics/kraken2/_format.py
q2_types_genomics/kraken2/_transformer.py
q2_types_genomics/kraken2/_type.py
q2_types_genomics/kraken2/tests/__init__.py
q2_types_genomics/kraken2/tests/test_format.py
q2_types_genomics/kraken2/tests/test_transformers.py
q2_types_genomics/kraken2/tests/test_type.py
q2_types_genomics/kraken2/tests/data/report-ok-table.csv
q2_types_genomics/kraken2/tests/data/bracken-db/database100mers.kmer_distrib
q2_types_genomics/kraken2/tests/data/bracken-db/database150mers.kmer_distrib
q2_types_genomics/kraken2/tests/data/kraken2-db/hash.k2d
q2_types_genomics/kraken2/tests/data/kraken2-db/opts.k2d
q2_types_genomics/kraken2/tests/data/kraken2-db/taxo.k2d
q2_types_genomics/kraken2/tests/data/outputs-mags/sample1/bin1_output.txt
q2_types_genomics/kraken2/tests/data/outputs-mags/sample1/bin2_output.txt
q2_types_genomics/kraken2/tests/data/outputs-mags/sample2/bin1_output.txt
q2_types_genomics/kraken2/tests/data/outputs-reads/sample1/output.txt
q2_types_genomics/kraken2/tests/data/outputs-reads/sample2/output.txt
q2_types_genomics/kraken2/tests/data/outputs-single/output-missing-column.txt
q2_types_genomics/kraken2/tests/data/outputs-single/output-ok.txt
q2_types_genomics/kraken2/tests/data/outputs-single/output-only-classified.txt
q2_types_genomics/kraken2/tests/data/outputs-single/output-wrong-first-col.txt
q2_types_genomics/kraken2/tests/data/reports-mags/sample1/bin1_report.txt
q2_types_genomics/kraken2/tests/data/reports-mags/sample1/bin2_report.txt
q2_types_genomics/kraken2/tests/data/reports-mags/sample2/bin1_report.txt
q2_types_genomics/kraken2/tests/data/reports-reads/sample1/report.txt
q2_types_genomics/kraken2/tests/data/reports-reads/sample2/report.txt
q2_types_genomics/kraken2/tests/data/reports-single/report-missing-column.txt
q2_types_genomics/kraken2/tests/data/reports-single/report-ok.txt
q2_types_genomics/kraken2/tests/data/reports-single/report-wrong-types.txt
q2_types_genomics/per_sample_data/__init__.py
q2_types_genomics/per_sample_data/_format.py
q2_types_genomics/per_sample_data/_transformer.py
q2_types_genomics/per_sample_data/_type.py
q2_types_genomics/per_sample_data/_util.py
q2_types_genomics/per_sample_data/tests/__init__.py
q2_types_genomics/per_sample_data/tests/test_format.py
q2_types_genomics/per_sample_data/tests/test_transformers.py
q2_types_genomics/per_sample_data/tests/test_type.py
q2_types_genomics/per_sample_data/tests/data/bowtie/index-unorganized/contigs.1.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-unorganized/contigs.2.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-unorganized/contigs.3.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-unorganized/contigs.4.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-unorganized/contigs.rev.1.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-unorganized/contigs.rev.2.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample1/mag1/contigs.1.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample1/mag1/contigs.2.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample1/mag1/contigs.3.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample1/mag1/contigs.4.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample1/mag1/contigs.rev.1.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample1/mag1/contigs.rev.2.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample2/mag1/contigs.1.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample2/mag1/contigs.2.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample2/mag1/contigs.3.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample2/mag1/contigs.4.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample2/mag1/contigs.rev.1.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/index-valid/sample2/mag1/contigs.rev.2.bt2
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-invalid/sample1.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-invalid/sample2.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-multi/sample1/map1.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-multi/sample1/map2.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-multi/sample2/map1.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-multi/sample2/map2.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-single/sample1.bam
q2_types_genomics/per_sample_data/tests/data/bowtie/maps-single/sample2.bam
q2_types_genomics/per_sample_data/tests/data/contigs/sample1_contigs.fa
q2_types_genomics/per_sample_data/tests/data/contigs/sample2_contigs.fa
q2_types_genomics/per_sample_data/tests/data/contigs/sample3_contigs.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-fa/sample1/mag1.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-fa/sample1/mag2.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-fa/sample1/mag3.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-fa/sample2/mag1.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-fa/sample2/mag2.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-fasta/sample1/mag1.fasta
q2_types_genomics/per_sample_data/tests/data/mags/mags-fasta/sample1/mag2.fasta
q2_types_genomics/per_sample_data/tests/data/mags/mags-fasta/sample1/mag3.fasta
q2_types_genomics/per_sample_data/tests/data/mags/mags-fasta/sample2/mag1.fasta
q2_types_genomics/per_sample_data/tests/data/mags/mags-fasta/sample2/mag2.fasta
q2_types_genomics/per_sample_data/tests/data/mags/mags-unorganized/mag1.fa
q2_types_genomics/per_sample_data/tests/data/mags/mags-unorganized/mag2.fa
q2_types_genomics/per_sample_data/tests/data/manifests/MANIFEST-empty
q2_types_genomics/per_sample_data/tests/data/manifests/MANIFEST-mags-fa
q2_types_genomics/per_sample_data/tests/data/manifests/MANIFEST-missing-column
q2_types_genomics/per_sample_data/tests/data/manifests/MANIFEST-missing-filepath
q2_types_genomics/per_sample_data/tests/data/manifests/MANIFEST-no-samples
q2_types_genomics/reference_db/__init__.py
q2_types_genomics/reference_db/_format.py
q2_types_genomics/reference_db/_type.py
q2_types_genomics/reference_db/tests/__init__.py
q2_types_genomics/reference_db/tests/test_format.py
q2_types_genomics/reference_db/tests/test_type.py
q2_types_genomics/reference_db/tests/data/bad_dmnd_db/bad_name.dmnd
q2_types_genomics/reference_db/tests/data/dmnd_db/ref_db.dmnd
q2_types_genomics/reference_db/tests/data/good_eggnog/eggnog.db
q2_types_genomics/reference_db/tests/data/good_eggnog/eggnog.taxa.db
q2_types_genomics/reference_db/tests/data/good_eggnog/eggnog.taxa.db.traverse.pkl
q2_types_genomics/reference_db/tests/data/single_eggnog/eggnog.db