CHANGELOG.md
LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
src/app/__init__.py
src/app/msstitch.py
src/app/actions/__init__.py
src/app/actions/merge.py
src/app/actions/proteins.py
src/app/actions/psmtopeptable.py
src/app/actions/sequence.py
src/app/actions/lookups/__init__.py
src/app/actions/lookups/quant.py
src/app/actions/lookups/sequence.py
src/app/actions/lookups/spectra.py
src/app/actions/percolator/__init__.py
src/app/actions/percolator/filters.py
src/app/actions/percolator/split.py
src/app/actions/psmtable/__init__.py
src/app/actions/psmtable/filtering.py
src/app/actions/psmtable/isosummarize.py
src/app/actions/psmtable/luciphor.py
src/app/actions/psmtable/percolator.py
src/app/actions/psmtable/refine.py
src/app/actions/psmtable/splitmerge.py
src/app/dataformats/__init__.py
src/app/dataformats/mzidtsv.py
src/app/dataformats/peptable.py
src/app/dataformats/prottable.py
src/app/dataformats/qvality.py
src/app/drivers/__init__.py
src/app/drivers/base.py
src/app/drivers/lookups.py
src/app/drivers/merge.py
src/app/drivers/options.py
src/app/drivers/peptable.py
src/app/drivers/percolator.py
src/app/drivers/prottable.py
src/app/drivers/psmtable.py
src/app/drivers/sequence.py
src/app/drivers/startup.py
src/app/lookups/__init__.py
src/app/lookups/base.py
src/app/lookups/sqlite/__init__.py
src/app/lookups/sqlite/base.py
src/app/lookups/sqlite/biosets.py
src/app/lookups/sqlite/peptable.py
src/app/lookups/sqlite/protpeptable.py
src/app/lookups/sqlite/prottable.py
src/app/lookups/sqlite/psms.py
src/app/lookups/sqlite/quant.py
src/app/lookups/sqlite/searchspace.py
src/app/lookups/sqlite/spectra.py
src/app/readers/__init__.py
src/app/readers/fasta.py
src/app/readers/mzidplus.py
src/app/readers/openms.py
src/app/readers/percolator.py
src/app/readers/spectra.py
src/app/readers/tsv.py
src/app/readers/xml.py
src/app/readers/xmlformatting.py
src/app/writers/__init__.py
src/app/writers/percolator.py
src/app/writers/tsv.py
src/msstitch.egg-info/PKG-INFO
src/msstitch.egg-info/SOURCES.txt
src/msstitch.egg-info/dependency_links.txt
src/msstitch.egg-info/entry_points.txt
src/msstitch.egg-info/requires.txt
src/msstitch.egg-info/top_level.txt
tests/__init__.py
tests/base_fixtures/ens99_small.fasta
tests/base_fixtures/few_spec_timstof.mzML
tests/base_fixtures/few_spectra.mzML
tests/base_fixtures/known_peptide_lookup.sqlite
tests/base_fixtures/proteins.fasta
tests/base_fixtures/rev_known_peptide_lookup.sqlite
tests/base_fixtures/twoproteins.fasta
tests/fixtures/decoy_peptides.tsv
tests/fixtures/decoy_tryprev_minlen_twoproteins.fasta
tests/fixtures/decoy_tryprev_pretryp_keeptarget_twoproteins.fasta
tests/fixtures/decoy_tryprev_pretryp_twoproteins.fasta
tests/fixtures/decoy_tryprev_targetcheck_twoproteins.fasta
tests/fixtures/decoy_tryprev_tcheck_keeptarget_twoproteins.fasta
tests/fixtures/decoy_tryprev_twoproteins.fasta
tests/fixtures/decoy_twoproteins.fasta
tests/fixtures/decoycheck.sqlite
tests/fixtures/dinoquant_lookup.sqlite
tests/fixtures/ensg.txt
tests/fixtures/ensg_nopsms.txt
tests/fixtures/few_spec_timstof.consXML
tests/fixtures/few_spec_timstof.mzid
tests/fixtures/few_spec_timstof.tsv
tests/fixtures/few_spec_timstof.tsv_fdr.tsv
tests/fixtures/few_spectra.consXML
tests/fixtures/few_spectra.kr
tests/fixtures/few_spectra.mzid
tests/fixtures/few_spectra.tsv
tests/fixtures/few_spectra.tsv_fdr.tsv
tests/fixtures/few_spectra_duplicate.tsv
tests/fixtures/genenames.txt
tests/fixtures/isosum_charge_column.txt
tests/fixtures/perco.xml
tests/fixtures/perco.xml_h0.xml
tests/fixtures/perco.xml_h1.xml
tests/fixtures/perco_duplicate.xml
tests/fixtures/perco_timstof.xml
tests/fixtures/proteins.txt
tests/fixtures/proteins_avg.txt
tests/fixtures/proteins_denoms_pickfdr.txt
tests/fixtures/proteins_intensities.txt
tests/fixtures/proteins_isonorm_log.txt
tests/fixtures/proteins_isonorm_nolog.txt
tests/fixtures/proteins_nonorm_log.txt
tests/fixtures/proteins_quantonly.txt
tests/fixtures/proteins_quantonly_splitmulti.txt
tests/fixtures/proteins_sweep.txt
tests/fixtures/protrev_ens99_small.fasta
tests/fixtures/quant_lookup.sqlite
tests/fixtures/qvality_peps.txt
tests/fixtures/qvality_psms.txt
tests/fixtures/set1_target_pg.tsv
tests/fixtures/spectra_lookup.sqlite
tests/fixtures/spectra_lookup_timstof.sqlite
tests/fixtures/target.tsv
tests/fixtures/target_pep_quant_norm.tsv
tests/fixtures/target_peptides.tsv
tests/fixtures/target_peptides_avg.tsv
tests/fixtures/target_peptides_sweep.tsv
tests/fixtures/target_peptides_totalp_sepnorm.txt
tests/fixtures/target_peptides_totalprotnorm.txt
tests/fixtures/target_peptides_totalprotnorm_nolog.txt
tests/fixtures/target_pg.tsv
tests/fixtures/target_psms.sqlite
tests/fixtures/trypsinized_twoproteins.fasta
tests/integration/__init__.py
tests/integration/basetests.py
tests/integration/merge_tests.py
tests/integration/mslookup_tests.py
tests/integration/peptable_tests.py
tests/integration/percolator_tests.py
tests/integration/psmtable_tests.py