.flake8
.zenodo.json
CHANGELOG.rst
CONTRIBUTING.rst
INSTALL.rst
LICENSE.rst
MANIFEST.in
README.rst
requirements-ext.txt
requirements.txt
setup.py
database/2021-11-22-ITS_Oomycota_w32.fasta
database/ITS1_DB.sql
database/Nothophytophthora_ITS1_curated.fasta
database/Phytophthora_ITS1_curated.fasta
database/README.rst
database/build_ITS1_DB.sh
database/controls.fasta
database/single_isolates/2019-BL-1B_S117_L001.fasta
database/single_isolates/2019-Pp2_S176_L001.fasta
database/single_isolates/75-BT3-1gDNA-P-austrocedrae-F08_S68_L001.fasta
database/single_isolates/76-GA3-1gDNA-P-austrocedrae-G08_S80_L001.fasta
database/single_isolates/78-CPB-DNA-from-FR-dil-1-100-P-obscura-H08_S92_L001.fasta
database/single_isolates/88069-P-infestans-56-A04_S4_L001.fasta
database/single_isolates/P-Europaea-DNA-from-FR-dil-1-100-F07_S67_L001.fasta
database/single_isolates/P-cinnamomi-82-1-10-A07_S7_L001.fasta
database/single_isolates/P-foliorum-DNA-from-FR-81-D08_S44_L001.fasta
database/single_isolates/P-foliorum_S165_L001.fasta
database/single_isolates/Pd2c_S105_L001.fasta
database/single_isolates/RG161_S139_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-1-C03_S27_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-1-G01_S73_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-2-D03_S39_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-2-D10_S46_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-2-H01_S85_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-3-A02_S2_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-3-E03_S51_L001.fasta
database/single_isolates/SCRP-1161-P-austrocedrae-3-E10_S58_L001.fasta
database/single_isolates/SCRP-1163-P-gonapodyides-C06_S30_L001.fasta
database/single_isolates/SCRP-1170-P-Erythroseptica-B08_S20_L001.fasta
database/single_isolates/SCRP-1171-P-Erythroseptica-C08_S32_L001.fasta
database/single_isolates/SCRP-1197-P-nicotianae-50-or-51-C04_S28_L001.fasta
database/single_isolates/SCRP-390-1-or-2-P-lateralis-G07_S79_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-1-D01_S37_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-1-H02_S86_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-2-A03_S3_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-2-A10_S10_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-2-E01_S49_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-3-B03_S15_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-3-B10_S22_L001.fasta
database/single_isolates/SCRP-734-P-pseudosyringae-3-F01_S61_L001.fasta
database/single_isolates/SCRP10-P-aln-G06_S78_L001.fasta
database/single_isolates/SCRP1022-P-capsici-40-B05_S17_L001.fasta
database/single_isolates/SCRP1161-P-austrocedrae-1-20-1-C10_S34_L001.fasta
database/single_isolates/SCRP1162-P-austrocedrae-E08_S56_L001.fasta
database/single_isolates/SCRP1218_S174_L001.fasta
database/single_isolates/SCRP1220_S151_L001.fasta
database/single_isolates/SCRP1222_S187_L001.fasta
database/single_isolates/SCRP1226_S186_L001.fasta
database/single_isolates/SCRP1227_S103_L001.fasta
database/single_isolates/SCRP165-P-citricola-T-60-D05_S41_L001.fasta
database/single_isolates/SCRP179-P-citrophthora-58-C05_S29_L001.fasta
database/single_isolates/SCRP179_S177_L001.fasta
database/single_isolates/SCRP207-P-Cryptogea-72-or-73-A08_S8_L001.fasta
database/single_isolates/SCRP23-P-boehmeriae-1-B09_S21_L001.fasta
database/single_isolates/SCRP231-P-cajani-71-1-10-C07_S31_L001.fasta
database/single_isolates/SCRP333-P-rubi-race-3-45-E07_S55_L001.fasta
database/single_isolates/SCRP35-1-or-2-P-cactorum-CAC17-R222-E04_S52_L001.fasta
database/single_isolates/SCRP37-P-cactorum-CAC19-145H-F04_S64_L001.fasta
database/single_isolates/SCRP371-P-idaei-41-A05_S5_L001.fasta
database/single_isolates/SCRP372-P-idaei-47-H04_S88_L001.fasta
database/single_isolates/SCRP377-P-ilicis-62-E05_S53_L001.fasta
database/single_isolates/SCRP386-P-iranica-48-D04_S40_L001.fasta
database/single_isolates/SCRP388-P-castaneae-44-H05_S89_L001.fasta
database/single_isolates/SCRP390_S129_L001.fasta
database/single_isolates/SCRP417-1-OR-2-P-megasperma-B06_S18_L001.fasta
database/single_isolates/SCRP420-P-megasperma-66-A06_S6_L001.fasta
database/single_isolates/SCRP455-P-melonis-70-B07_S19_L001.fasta
database/single_isolates/SCRP474-P-palmivora-11-F05_S65_L001.fasta
database/single_isolates/SCRP526-P-palmivora-64A-G05_S77_L001.fasta
database/single_isolates/SCRP538-P-pseudotsugae-54-B04_S16_L001.fasta
database/single_isolates/SCRP56-P-cactorum-CH97-46-G04_S76_L001.fasta
database/single_isolates/SCRP607-P-fallax-12-A09_S9_L001.fasta
database/single_isolates/SCRP645-P-inundata-68-D06_S42_L001.fasta
database/single_isolates/SCRP660-P-syringae-83-H07_S91_L001.fasta
database/single_isolates/SCRP660_S153_L001.fasta
database/single_isolates/SCRP71-P-cambivora-69-cam5-H06_S90_L001.fasta
database/single_isolates/SCRP722-P-kernoviae-84-dil-1-100-C09_S33_L001.fasta
database/single_isolates/SCRP722_S141_L001.fasta
database/single_isolates/SCRP734-1-or-2-P-pseudosyringae-1-H09_S93_L001.fasta
database/single_isolates/SCRP893-P-sojae-22-D07_S43_L001.fasta
database/single_isolates/SCRP9-P-aln-F06_S66_L001.fasta
database/single_isolates/SRCP1221_S175_L001.fasta
database/single_isolates/T-30-4-1-A01_S1_L001.fasta
database/single_isolates/T-30-4-1-E02_S50_L001.fasta
database/single_isolates/T-30-4-2-B01_S13_L001.fasta
database/single_isolates/T-30-4-2-F02_S62_L001.fasta
database/single_isolates/T-30-4-2-F09_S69_L001.fasta
database/single_isolates/T-30-4-3-C01_S25_L001.fasta
database/single_isolates/T-30-4-3-G02_S74_L001.fasta
database/single_isolates/T-30-4-3-G09_S81_L001.fasta
database/single_isolates/T30-4-P-infestans-55-1-20-1-E09_S57_L001.fasta
database/single_isolates/WL54_S128_L001.fasta
database/single_isolates/WL77_S152_L001.fasta
examples/README.rst
examples/endangered_species/PRJEB18620.tsv
examples/endangered_species/README.rst
examples/endangered_species/metadata.tsv
examples/endangered_species/run.sh
examples/endangered_species/setup.sh
examples/endangered_species/expected/EM_1.known.tsv
examples/endangered_species/expected/EM_10.known.tsv
examples/endangered_species/expected/EM_11.known.tsv
examples/endangered_species/expected/EM_12.known.tsv
examples/endangered_species/expected/EM_13.known.tsv
examples/endangered_species/expected/EM_14.known.tsv
examples/endangered_species/expected/EM_15.known.tsv
examples/endangered_species/expected/EM_2.known.tsv
examples/endangered_species/expected/EM_3.known.tsv
examples/endangered_species/expected/EM_4.known.tsv
examples/endangered_species/expected/EM_5.known.tsv
examples/endangered_species/expected/EM_6.known.tsv
examples/endangered_species/expected/EM_7.known.tsv
examples/endangered_species/expected/EM_8.known.tsv
examples/endangered_species/expected/EM_9.known.tsv
examples/endangered_species/expected/S1.template.tsv
examples/endangered_species/expected/S10.template.tsv
examples/endangered_species/expected/S2.template.tsv
examples/endangered_species/expected/S4.template.tsv
examples/endangered_species/expected/S5.template.tsv
examples/endangered_species/expected/S6.template.tsv
examples/endangered_species/expected/S7.template.tsv
examples/endangered_species/expected/S9.template.tsv
examples/endangered_species/raw_download/MD5SUM.txt
examples/endangered_species/references/16S.fasta
examples/endangered_species/references/ITS2.fasta
examples/endangered_species/references/Mini-16S.fasta
examples/endangered_species/references/Mini-COI.fasta
examples/endangered_species/references/Mini-cyt-b.fasta
examples/endangered_species/references/Mini-rbcL.fasta
examples/endangered_species/references/cyt-b.fasta
examples/endangered_species/references/rbcL.fasta
examples/endangered_species/references/trnL-P6-loop.fasta
examples/endangered_species/references/trnL-UAA.fasta
examples/fecal_sequel/PRJNA574765.tsv
examples/fecal_sequel/README.rst
examples/fecal_sequel/curated_bats.fasta
examples/fecal_sequel/metadata.tsv
examples/fecal_sequel/mock_community.known.tsv
examples/fecal_sequel/observed_3_bats.fasta
examples/fecal_sequel/run.sh
examples/fecal_sequel/setup.sh
examples/fecal_sequel/raw_data/MD5SUM.txt
examples/fungal_mock/ITS1.fasta
examples/fungal_mock/ITS2.fasta
examples/fungal_mock/PRJNA377530.tsv
examples/fungal_mock/README.rst
examples/fungal_mock/metadata_AL1.tsv
examples/fungal_mock/metadata_AL2.tsv
examples/fungal_mock/mock_community.known.tsv
examples/fungal_mock/negative_control.known.tsv
examples/fungal_mock/run.sh
examples/fungal_mock/setup.sh
examples/fungal_mock/raw_data/AL2/MD5SUM.txt
examples/great_lakes/MOL16S.fasta
examples/great_lakes/PRJNA379165.tsv
examples/great_lakes/README.rst
examples/great_lakes/SPH16S.fasta
examples/great_lakes/metadata.tsv
examples/great_lakes/run.sh
examples/great_lakes/setup.sh
examples/great_lakes/expected/mock_community.MOL16S.known.tsv
examples/great_lakes/expected/mock_community.SPH16S.known.tsv
examples/great_lakes/expected/negative_control.known.tsv
examples/great_lakes/raw_data/MD5SUM.txt
examples/recycled_water/PRJNA417859.tsv
examples/recycled_water/README.rst
examples/recycled_water/Redekar_et_al_2019_sup_table_3.fasta
examples/recycled_water/Redekar_et_al_2019_sup_table_3.tsv
examples/recycled_water/make_meta.py
examples/recycled_water/metadata.tsv
examples/recycled_water/run.sh
examples/recycled_water/setup.sh
examples/recycled_water/raw_data/MD5SUM.txt
examples/soil_nematodes/PRJEB27581.tsv
examples/soil_nematodes/README.rst
examples/soil_nematodes/metadata.tsv
examples/soil_nematodes/mock_community.known.tsv
examples/soil_nematodes/negative_control.known.tsv
examples/soil_nematodes/run.sh
examples/soil_nematodes/setup.sh
examples/soil_nematodes/raw_data/MD5SUM.txt
examples/woody_hosts/README.rst
examples/woody_hosts/metadata.tsv
examples/woody_hosts/run.sh
examples/woody_hosts/setup.sh
examples/woody_hosts/expected/DNA10MIX_bycopynumber.known.tsv
examples/woody_hosts/expected/DNA10MIX_diluted25x.known.tsv
examples/woody_hosts/expected/DNA10MIX_undiluted.known.tsv
examples/woody_hosts/expected/DNA15MIX.known.tsv
scripts/README.rst
scripts/blast_to_fasta.py
scripts/make_nr.py
scripts/md5.py
scripts/pooling.py
scripts/rst_doc_test.py
tests/run_tests.sh
tests/test_assess.sh
tests/test_build_db.sh
tests/test_classify.sh
tests/test_conflicts.sh
tests/test_curated-import.sh
tests/test_curated-seq.sh
tests/test_dump.sh
tests/test_edit-graph.sh
tests/test_ena-submit.sh
tests/test_fasta-nr.sh
tests/test_load-tax.sh
tests/test_marker_clash.sh
tests/test_multi_marker.sh
tests/test_ncbi-import.sh
tests/test_pipeline.sh
tests/test_pooling.sh
tests/test_prepare-reads.sh
tests/test_summary.sh
tests/test_synthetic_controls.sh
tests/test_woody_hosts.sh
tests/assess/ex1.assess.tsv
tests/assess/ex1.identity.tsv
tests/assess/ex1.known.tsv
tests/assess/ex1a.identity.tsv
tests/assess/ex1a.known.tsv
tests/assess/ex2.assess.tsv
tests/assess/ex2.identity.tsv
tests/assess/ex2.known.tsv
tests/assess/ex3.assess.tsv
tests/assess/ex3.identity.tsv
tests/assess/ex3.known.tsv
tests/assess/ex4.assess.tsv
tests/assess/ex4.identity.tsv
tests/assess/ex4.known.tsv
tests/assess/fp.assess.tsv
tests/assess/fp.identity.tsv
tests/assess/fp.known.tsv
tests/assess/meta.tsv
tests/assess/samples.assess.tsv
tests/assess/samples.confusion.tsv
tests/assess/samples.tally.tsv
tests/assess/seven.fasta
tests/assess/unclassified.assess.tsv
tests/assess/unclassified.identity.tsv
tests/assess/unclassified.known.tsv
tests/classifier/P_bilorbang.fasta
tests/classifier/P_bilorbang_query.1s2g.tsv
tests/classifier/P_bilorbang_query.1s3g.tsv
tests/classifier/P_bilorbang_query.1s4g.tsv
tests/classifier/P_bilorbang_query.1s5g.tsv
tests/classifier/P_bilorbang_query.fasta
tests/classifier/P_bilorbang_query.identity.tsv
tests/classifier/P_bilorbang_query.onebp.tsv
tests/classifier/P_vulcanica.fasta
tests/classifier/P_vulcanica_query.1s2g.tsv
tests/classifier/P_vulcanica_query.1s3g.tsv
tests/classifier/P_vulcanica_query.1s4g.tsv
tests/classifier/P_vulcanica_query.1s5g.tsv
tests/classifier/P_vulcanica_query.fasta
tests/classifier/P_vulcanica_query.identity.tsv
tests/classifier/P_vulcanica_query.onebp.tsv
tests/classifier/corner_cases_query.1s2g.tsv
tests/classifier/corner_cases_query.1s3g.tsv
tests/classifier/corner_cases_query.1s4g.tsv
tests/classifier/corner_cases_query.1s5g.tsv
tests/classifier/corner_cases_query.blast.tsv
tests/classifier/corner_cases_query.fasta
tests/classifier/corner_cases_query.identity.tsv
tests/classifier/corner_cases_query.onebp.tsv
tests/classifier/genus_boundary.fasta
tests/classifier/genus_boundary_query.1s2g.tsv
tests/classifier/genus_boundary_query.1s3g.tsv
tests/classifier/genus_boundary_query.1s4g.tsv
tests/classifier/genus_boundary_query.1s5g.tsv
tests/classifier/genus_boundary_query.fasta
tests/classifier/genus_boundary_query.identity.tsv
tests/classifier/genus_boundary_query.onebp.tsv
tests/classify/P-infestans-T30-4.1s3g.tsv
tests/classify/P-infestans-T30-4.blast.tsv
tests/classify/P-infestans-T30-4.fasta
tests/classify/P-infestans-T30-4.identity.tsv
tests/classify/P-infestans-T30-4.meta.tsv
tests/classify/P-infestans-T30-4.onebp.tsv
tests/classify/P-infestans-T30-4.reads.tsv
tests/classify/P-infestans-T30-4.samples.tsv
tests/classify/P-infestans-T30-4.substr.tsv
tests/classify/P-infestans-etc.meta.tsv
tests/classify/P-infestans-etc.reads.tsv
tests/classify/P-infestans-etc.samples.tsv
tests/classify/hmm_trim.1s3g.tsv
tests/classify/hmm_trim.blast.tsv
tests/classify/hmm_trim.fasta
tests/classify/hmm_trim.identity.tsv
tests/classify/hmm_trim.onebp.tsv
tests/conflicts/default.tsv
tests/conflicts/dup_seqs.tsv
tests/curated-import/dup_seqs.fasta
tests/edit-graph/DNAMIX_S95_L001.tsv
tests/edit-graph/DNAMIX_S95_L001.xgmml
tests/marker_clash/GBLOCK-example.ITS1.1s2g.tsv
tests/marker_clash/GBLOCK-example.ITS1.1s3g.tsv
tests/marker_clash/GBLOCK-example.ITS1.1s4g.tsv
tests/marker_clash/GBLOCK-example.ITS1.1s5g.tsv
tests/marker_clash/GBLOCK-example.ITS1.blast.tsv
tests/marker_clash/GBLOCK-example.ITS1.identity.tsv
tests/marker_clash/GBLOCK-example.ITS1.onebp.tsv
tests/marker_clash/GBLOCK-example.ITS1.substr.tsv
tests/marker_clash/GBLOCK-example.NotITS1.tsv
tests/marker_clash/GBLOCK-example.fasta
tests/marker_clash/Phytophthora_cinnamomi.fasta
tests/marker_clash/conflicts.tsv
tests/multi_marker/README.rst
tests/multi_marker/intermediate/16S/EM_1_sample.fasta
tests/multi_marker/intermediate/ITS2/EM_1_sample.fasta
tests/multi_marker/intermediate/Mini-16S/EM_1_sample.fasta
tests/multi_marker/intermediate/Mini-COI/EM_1_sample.fasta
tests/multi_marker/intermediate/Mini-cyt-b/EM_1_sample.fasta
tests/multi_marker/intermediate/Mini-rbcL/EM_1_sample.fasta
tests/multi_marker/intermediate/rbcL/EM_1_sample.fasta
tests/multi_marker/intermediate/trnL-P6-loop/EM_1_sample.fasta
tests/multi_marker/intermediate/trnL-UAA/EM_1_sample.fasta
tests/multi_marker/raw_data/EM_1_sample_R1.fastq.gz
tests/multi_marker/raw_data/EM_1_sample_R2.fastq.gz
tests/multi_marker/summary/pooled.reads.onebp.tsv
tests/multi_marker/summary/pooled.samples.onebp.tsv
tests/ncbi-import/20th_Century_ITS1.fasta
tests/ncbi-import/20th_Century_ITS1_Peronosporaceae.fasta
tests/ncbi-import/hybrid.fasta
tests/ncbi-import/multiple_hmm.fasta
tests/nematodes/README.rst
tests/nematodes/sample_R1.fastq.gz
tests/nematodes/sample_R2.fastq.gz
tests/nematodes/sample_flip_a10.fasta
tests/nematodes/sample_noflip_a10.fasta
tests/pipeline/thapbi-pict.all_reads.fasta
tests/pipeline/thapbi-pict.reads.onebp.tsv
tests/pipeline/thapbi-pict.samples.onebp.tsv
tests/pipeline/thapbi-pict.samples.onebp.txt
tests/pooling/example.pooled.tsv
tests/pooling/example.samples.onebp.tsv
tests/prepare-reads/6e847180a4da6eed316e1fb98b21218f.fasta
tests/prepare-reads/DNAMIX_S95_L001.fasta
tests/prepare-reads/DNAMIX_S95_L001.swarmid.tsv
tests/prepare-reads/SRR6303948_sample_default.fasta
tests/prepare-reads/SRR6303948_sample_primers.fasta
tests/reads/6e847180a4da6eed316e1fb98b21218f_R1.fastq
tests/reads/6e847180a4da6eed316e1fb98b21218f_R1.fastq.md5
tests/reads/6e847180a4da6eed316e1fb98b21218f_R2.fastq
tests/reads/6e847180a4da6eed316e1fb98b21218f_R2.fastq.md5
tests/reads/DNAMIX_S95_L001_R1_001.fastq.gz
tests/reads/DNAMIX_S95_L001_R1_001.fastq.gz.md5
tests/reads/DNAMIX_S95_L001_R2_001.fastq.gz
tests/reads/DNAMIX_S95_L001_R2_001.fastq.gz.md5
tests/reads/SRR6303948_sample_1.fastq
tests/reads/SRR6303948_sample_1.fastq.md5
tests/reads/SRR6303948_sample_2.fastq
tests/reads/SRR6303948_sample_2.fastq.md5
tests/reads/ena_submit.tsv
tests/reads/ena_submit_custom.tsv
tests/reads/metadata.tsv
tests/summary/assess-meta.identity.tsv
tests/summary/assess-meta.identity.txt
tests/summary/assess.identity.tsv
tests/summary/assess.identity.txt
tests/summary/classify-meta-req.blast.tsv
tests/summary/classify-meta-req.blast.txt
tests/summary/classify-meta-req.identity.tsv
tests/summary/classify-meta-req.identity.txt
tests/summary/classify-meta-req.onebp.tsv
tests/summary/classify-meta-req.onebp.txt
tests/summary/classify-meta-req.swarm.tsv
tests/summary/classify-meta-req.swarm.txt
tests/summary/classify-meta-req.swarmid.tsv
tests/summary/classify-meta-req.swarmid.txt
tests/summary/classify-meta.blast.tsv
tests/summary/classify-meta.blast.txt
tests/summary/classify-meta.identity.tsv
tests/summary/classify-meta.identity.txt
tests/summary/classify-meta.onebp.tsv
tests/summary/classify-meta.onebp.txt
tests/summary/classify-meta.swarm.tsv
tests/summary/classify-meta.swarm.txt
tests/summary/classify-meta.swarmid.tsv
tests/summary/classify-meta.swarmid.txt
tests/summary/classify.blast.tsv
tests/summary/classify.blast.txt
tests/summary/classify.identity.tsv
tests/summary/classify.identity.txt
tests/summary/classify.onebp.tsv
tests/summary/classify.onebp.txt
tests/summary/classify.swarm.tsv
tests/summary/classify.swarm.txt
tests/summary/classify.swarmid.tsv
tests/summary/classify.swarmid.txt
tests/summary_meta/A1.1s3g.tsv
tests/summary_meta/A1.fasta
tests/summary_meta/A2.1s3g.tsv
tests/summary_meta/A2.fasta
tests/summary_meta/B1.1s3g.tsv
tests/summary_meta/B1.fasta
tests/summary_meta/B1r.1s3g.tsv
tests/summary_meta/B1r.fasta
tests/summary_meta/C1.1s3g.tsv
tests/summary_meta/C1.fasta
tests/summary_meta/X1.1s3g.tsv
tests/summary_meta/X1.fasta
tests/summary_meta/Y1.1s3g.tsv
tests/summary_meta/Y1.fasta
tests/summary_meta/metadata.tsv
tests/summary_meta/summary-q.reads.1s3g.tsv
tests/summary_meta/summary-q.samples.1s3g.tsv
tests/summary_meta/summary-q.samples.1s3g.txt
tests/summary_meta/summary-qu.samples.1s3g.tsv
tests/summary_meta/summary-qu.samples.1s3g.txt
tests/summary_meta/summary-u.samples.1s3g.tsv
tests/summary_meta/summary-u.samples.1s3g.txt
tests/summary_meta/summary.reads.1s3g.tsv
tests/summary_meta/summary.samples.1s3g.tsv
tests/summary_meta/summary.samples.1s3g.txt
tests/synthetic_controls/report.ITS1.all_reads.1s3g.tsv
tests/synthetic_controls/report.ITS1.reads.1s3g.tsv
tests/synthetic_controls/report.ITS1.samples.1s3g.tsv
tests/synthetic_controls/spike-in-A.fasta
tests/synthetic_controls/spike-in-B.fasta
tests/synthetic_controls/spike-in-C.fasta
tests/synthetic_controls/spike-in-D.fasta
tests/woody_hosts/DNA_MIXES.assess.tsv
tests/woody_hosts/README.rst
tests/woody_hosts/all.fasta
tests/woody_hosts/all.identity.tsv
tests/woody_hosts/all.onebp.tsv
tests/woody_hosts/intermediate.tar.bz2
thapbi_pict/ITS1_DB.sqlite
thapbi_pict/__init__.py
thapbi_pict/__main__.py
thapbi_pict/assess.py
thapbi_pict/classify.py
thapbi_pict/conflicts.py
thapbi_pict/db_import.py
thapbi_pict/db_orm.py
thapbi_pict/dump.py
thapbi_pict/edit_graph.py
thapbi_pict/ena_submit.py
thapbi_pict/fasta_nr.py
thapbi_pict/prepare.py
thapbi_pict/seq_import.py
thapbi_pict/summary.py
thapbi_pict/taxdump.py
thapbi_pict/utils.py
thapbi_pict/versions.py
thapbi_pict.egg-info/PKG-INFO
thapbi_pict.egg-info/SOURCES.txt
thapbi_pict.egg-info/dependency_links.txt
thapbi_pict.egg-info/entry_points.txt
thapbi_pict.egg-info/requires.txt
thapbi_pict.egg-info/top_level.txt