CHANGELOG.rst
CONTRIBUTING.rst
INSTALL.rst
LICENSE.rst
MANIFEST.in
README.rst
setup.py
database/ITS1_DB.sql
database/Phytophthora_ITS1_curated.fasta
database/README.rst
database/controls.fasta
examples/README.rst
examples/fungal_mock/ITS1.fasta
examples/fungal_mock/ITS2.fasta
examples/fungal_mock/PRJNA377530.txt
examples/fungal_mock/README.rst
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/amp_lib_one/metadata.tsv
examples/fungal_mock/amp_lib_one/raw_data/MD5SUM.txt
examples/fungal_mock/amp_lib_two/metadata.tsv
examples/fungal_mock/amp_lib_two/raw_data/MD5SUM.txt
examples/microalgal_mock/PRJNA314977.txt
examples/microalgal_mock/README.rst
examples/microalgal_mock/metadata.tsv
examples/microalgal_mock/mock_community.fasta
examples/microalgal_mock/mock_community.known.tsv
examples/microalgal_mock/mock_freshwater.known.tsv
examples/microalgal_mock/mock_marine.known.tsv
examples/microalgal_mock/run.sh
examples/microalgal_mock/setup.sh
examples/microalgal_mock/V4/raw_data/MD5SUM.txt
examples/microalgal_mock/V8V9/raw_data/MD5SUM.txt
examples/recycled_water/PRJNA417859.txt
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/woody_hosts/README.rst
examples/woody_hosts/intermediate.tar.bz2
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
tests/run_tests.sh
tests/test_assess.sh
tests/test_classify.sh
tests/test_conflicts.sh
tests/test_curated-import.sh
tests/test_dump.sh
tests/test_edit-graph.sh
tests/test_fasta-nr.sh
tests/test_load-tax.sh
tests/test_ncbi-import.sh
tests/test_pipeline.sh
tests/test_prepare-reads.sh
tests/test_read-summary.sh
tests/test_sample-summary.sh
tests/test_seq-import.sh
tests/test_woody_hosts.sh
tests/assess/assess_sample.tsv
tests/assess/assess_sseq.tsv
tests/assess/assess_useq.tsv
tests/assess/confusion_sample.tsv
tests/assess/confusion_sseq.tsv
tests/assess/confusion_useq.tsv
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/tally_sample.tsv
tests/assess/tally_sseq.tsv
tests/assess/tally_useq.tsv
tests/assess/unclassified.assess.tsv
tests/assess/unclassified.identity.tsv
tests/assess/unclassified.known.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.summary.tsv
tests/classify/P-infestans-T30-4.swarm.tsv
tests/classify/P-infestans-T30-4.swarmid.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/classify/multiple_its1.blast.tsv
tests/classify/multiple_its1.fasta
tests/classify/multiple_its1.identity.tsv
tests/classify/multiple_its1.onebp.tsv
tests/conflicts/default.tsv
tests/conflicts/dup_seqs.tsv
tests/curated-import/dup_seqs.fasta
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/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.edit-graph.xgmml
tests/pipeline/thapbi-pict.reads.onebp.tsv
tests/pipeline/thapbi-pict.samples.onebp.tsv
tests/pipeline/thapbi-pict.samples.onebp.txt
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/DNAMIX_S95_L001_R1_001.fastq.gz
tests/reads/DNAMIX_S95_L001_R2_001.fastq.gz
tests/reads/SRR6303948_sample_1.fastq
tests/reads/SRR6303948_sample_2.fastq
tests/sample-summary/assess-meta.identity.tsv
tests/sample-summary/assess-meta.identity.txt
tests/sample-summary/assess.identity.tsv
tests/sample-summary/assess.identity.txt
tests/sample-summary/classify-meta-req.blast.tsv
tests/sample-summary/classify-meta-req.blast.txt
tests/sample-summary/classify-meta-req.identity.tsv
tests/sample-summary/classify-meta-req.identity.txt
tests/sample-summary/classify-meta-req.onebp.tsv
tests/sample-summary/classify-meta-req.onebp.txt
tests/sample-summary/classify-meta-req.swarm.tsv
tests/sample-summary/classify-meta-req.swarm.txt
tests/sample-summary/classify-meta-req.swarmid.tsv
tests/sample-summary/classify-meta-req.swarmid.txt
tests/sample-summary/classify-meta.blast.tsv
tests/sample-summary/classify-meta.blast.txt
tests/sample-summary/classify-meta.identity.tsv
tests/sample-summary/classify-meta.identity.txt
tests/sample-summary/classify-meta.onebp.tsv
tests/sample-summary/classify-meta.onebp.txt
tests/sample-summary/classify-meta.swarm.tsv
tests/sample-summary/classify-meta.swarm.txt
tests/sample-summary/classify-meta.swarmid.tsv
tests/sample-summary/classify-meta.swarmid.txt
tests/sample-summary/classify.blast.tsv
tests/sample-summary/classify.blast.txt
tests/sample-summary/classify.identity.tsv
tests/sample-summary/classify.identity.txt
tests/sample-summary/classify.onebp.tsv
tests/sample-summary/classify.onebp.txt
tests/sample-summary/classify.swarm.tsv
tests/sample-summary/classify.swarm.txt
tests/sample-summary/classify.swarmid.tsv
tests/sample-summary/classify.swarmid.txt
tests/woody_hosts/DNA_MIXES.assess.tsv
tests/woody_hosts/all.blast.tsv
tests/woody_hosts/all.fasta
tests/woody_hosts/all.identity.tsv
tests/woody_hosts/all.onebp.tsv
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/curated.py
thapbi_pict/db_import.py
thapbi_pict/db_orm.py
thapbi_pict/dump.py
thapbi_pict/edit_graph.py
thapbi_pict/fasta_nr.py
thapbi_pict/ncbi.py
thapbi_pict/prepare.py
thapbi_pict/read_summary.py
thapbi_pict/sample_summary.py
thapbi_pict/seq_import.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
thapbi_pict/hmm/__init__.py
thapbi_pict/hmm/controls.hmm
thapbi_pict/hmm/controls.hmm.h3f
thapbi_pict/hmm/controls.hmm.h3i
thapbi_pict/hmm/controls.hmm.h3m
thapbi_pict/hmm/controls.hmm.h3p