CHANGELOG.rst
CONTRIBUTING.rst
INSTALL.rst
LICENSE.rst
MANIFEST.in
README.rst
setup.py
database/ITS1_DB.sql
database/README.rst
database/legacy/Phytophthora_ITS_database_v0.004.fasta
database/legacy/Phytophthora_ITS_database_v0.005.fasta
database/legacy/Phytophthora_ITS_database_v0.006.fasta
database/legacy/database.fasta
tests/run_tests.sh
tests/test_assess.sh
tests/test_classify.sh
tests/test_conflicts.sh
tests/test_dump.sh
tests/test_edit-graph.sh
tests/test_legacy-import.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/264d8b113857804f072cb341c72bbdd0.fasta
tests/classify/8c4aec200c518fb2b124603c0d3babb5.fasta
tests/classify/Nothophytophthora.fasta
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/funny.fasta
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/legacy-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/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/reads/DNAMIX_S95_L001_R1_001.fastq.gz
tests/reads/DNAMIX_S95_L001_R2_001.fastq.gz
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.blast.txt
tests/sample-summary/classify-meta.identity.txt
tests/sample-summary/classify-meta.onebp.txt
tests/sample-summary/classify-meta.swarm.txt
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/woody_hosts/DNA10MIX_bycopynumber.known.tsv
tests/woody_hosts/DNA10MIX_diluted25x.known.tsv
tests/woody_hosts/DNA10MIX_undiluted.known.tsv
tests/woody_hosts/DNA15MIX.known.tsv
tests/woody_hosts/DNA_MIXES.assess.tsv
tests/woody_hosts/intermediate.tar.bz2
tests/woody_hosts/site_metadata.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/db_import.py
thapbi_pict/db_orm.py
thapbi_pict/dump.py
thapbi_pict/edit_graph.py
thapbi_pict/legacy.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/combined.hmm
thapbi_pict/hmm/combined.hmm.h3f
thapbi_pict/hmm/combined.hmm.h3i
thapbi_pict/hmm/combined.hmm.h3m
thapbi_pict/hmm/combined.hmm.h3p
thapbi_pict/hmm/phytophthora_its1.fas
thapbi_pict/hmm/phytophthora_its1.hmm
thapbi_pict/hmm/phytophthora_its1.sto
thapbi_pict/hmm/phytophthora_its1.txt