CHANGELOG.md
LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
src/app/__init__.py
src/app/mslookup.py
src/app/mzidtsv.py
src/app/peptable.py
src/app/prottable.py
src/app/pycolator.py
src/app/actions/__init__.py
src/app/actions/isonormalizing.py
src/app/actions/mergetable.py
src/app/actions/proteindata.py
src/app/actions/headers/__init__.py
src/app/actions/headers/base.py
src/app/actions/headers/peptable.py
src/app/actions/headers/prottable.py
src/app/actions/mslookup/__init__.py
src/app/actions/mslookup/biosets.py
src/app/actions/mslookup/proteingrouping.py
src/app/actions/mslookup/proteinquant.py
src/app/actions/mslookup/psms.py
src/app/actions/mslookup/quant.py
src/app/actions/mslookup/searchspace.py
src/app/actions/mslookup/spectra.py
src/app/actions/mzidtsv/__init__.py
src/app/actions/mzidtsv/confidencefilters.py
src/app/actions/mzidtsv/filter_confidence.py
src/app/actions/mzidtsv/isonormalize.py
src/app/actions/mzidtsv/percolator.py
src/app/actions/mzidtsv/prot2gene.py
src/app/actions/mzidtsv/proteingroup_sorters.py
src/app/actions/mzidtsv/proteingrouping.py
src/app/actions/mzidtsv/quant.py
src/app/actions/mzidtsv/spectra.py
src/app/actions/mzidtsv/splitmerge.py
src/app/actions/peptable/__init__.py
src/app/actions/peptable/base.py
src/app/actions/peptable/isoquant.py
src/app/actions/peptable/merge.py
src/app/actions/peptable/model_qvals.py
src/app/actions/peptable/psmtopeptable.py
src/app/actions/prottable/__init__.py
src/app/actions/prottable/bestpeptide.py
src/app/actions/prottable/create_empty.py
src/app/actions/prottable/fdr.py
src/app/actions/prottable/info.py
src/app/actions/prottable/isoquant.py
src/app/actions/prottable/merge.py
src/app/actions/prottable/picktdprotein.py
src/app/actions/prottable/precursorarea.py
src/app/actions/prottable/probability.py
src/app/actions/pycolator/__init__.py
src/app/actions/pycolator/filters.py
src/app/actions/pycolator/qvality.py
src/app/actions/pycolator/reassign.py
src/app/actions/pycolator/splitmerge.py
src/app/actions/shared/__init__.py
src/app/actions/shared/pepprot_isoquant.py
src/app/dataformats/__init__.py
src/app/dataformats/mzidtsv.py
src/app/dataformats/peptable.py
src/app/dataformats/prottable.py
src/app/drivers/__init__.py
src/app/drivers/base.py
src/app/drivers/options.py
src/app/drivers/pepprottable.py
src/app/drivers/startup.py
src/app/drivers/mslookup/__init__.py
src/app/drivers/mslookup/base.py
src/app/drivers/mslookup/biosets.py
src/app/drivers/mslookup/pepquant.py
src/app/drivers/mslookup/proteingroups.py
src/app/drivers/mslookup/proteinquant.py
src/app/drivers/mslookup/psms.py
src/app/drivers/mslookup/quant.py
src/app/drivers/mslookup/seqspace.py
src/app/drivers/mslookup/spectra.py
src/app/drivers/mzidtsv/__init__.py
src/app/drivers/mzidtsv/filter_confidence.py
src/app/drivers/mzidtsv/isonormalize.py
src/app/drivers/mzidtsv/percolator.py
src/app/drivers/mzidtsv/prot2gene.py
src/app/drivers/mzidtsv/proteingrouping.py
src/app/drivers/mzidtsv/quant.py
src/app/drivers/mzidtsv/spectra.py
src/app/drivers/mzidtsv/splitmerge.py
src/app/drivers/peptable/__init__.py
src/app/drivers/peptable/base.py
src/app/drivers/peptable/isoquant.py
src/app/drivers/peptable/merge.py
src/app/drivers/peptable/model_qvals.py
src/app/drivers/peptable/psmtopeptable.py
src/app/drivers/prottable/__init__.py
src/app/drivers/prottable/base.py
src/app/drivers/prottable/bestpeptide.py
src/app/drivers/prottable/create_empty.py
src/app/drivers/prottable/fdr.py
src/app/drivers/prottable/info.py
src/app/drivers/prottable/isoquant.py
src/app/drivers/prottable/merge.py
src/app/drivers/prottable/precursorarea.py
src/app/drivers/prottable/probability.py
src/app/drivers/pycolator/__init__.py
src/app/drivers/pycolator/base.py
src/app/drivers/pycolator/filters.py
src/app/drivers/pycolator/qvality.py
src/app/drivers/pycolator/splitmerge.py
src/app/drivers/pycolator/stats.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/proteingroups.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/ml.py
src/app/readers/mzidplus.py
src/app/readers/openms.py
src/app/readers/pycolator.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/mzidtsv.py
src/app/writers/prottable.py
src/app/writers/pycolator.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/fixtures/allpeptides_proteins.yml
tests/fixtures/biomart.map
tests/fixtures/bioset_lookup.sqlite
tests/fixtures/decoy_ensembl.fasta
tests/fixtures/decoy_ensembl_extrapep.fasta
tests/fixtures/delim_header.fasta
tests/fixtures/ensembl.fasta
tests/fixtures/ensembl_extrapep.fasta
tests/fixtures/ensembl_versioned.fasta
tests/fixtures/few_spectra.mzML
tests/fixtures/full_prottable.txt
tests/fixtures/known_peptide_lookup.sqlite
tests/fixtures/kronik.txt
tests/fixtures/msgfperco_fr0.mzid
tests/fixtures/mzidtsv.txt
tests/fixtures/mzidtsv_db.sqlite
tests/fixtures/mzidtsv_db_nopgroups.sqlite
tests/fixtures/mzidtsv_filtered_fr1-2.txt
tests/fixtures/mzidtsv_filtered_fr1-2_decoy.txt
tests/fixtures/mzidtsv_filtered_fr1-2_extrapep.txt
tests/fixtures/mzidtsv_filtered_fr1-2_extrapep_decoy.txt
tests/fixtures/mzidtsv_filtered_fr1-2_isonorm.txt
tests/fixtures/mzidtsv_filtered_fr1-2_nospecdata.txt
tests/fixtures/mzidtsv_filtered_fr1-2_notensembl.txt
tests/fixtures/mzidtsv_filtered_fr1-2_proteingrouped.txt
tests/fixtures/mzidtsv_filtered_fr1-2_versioned_ensembl.txt
tests/fixtures/mzidtsv_fr0.txt
tests/fixtures/mzidtsv_fr1.txt
tests/fixtures/mzidtsv_intensities.txt
tests/fixtures/mzidtsv_ratios.txt
tests/fixtures/mzidtsv_short.txt
tests/fixtures/mzidtsv_unrolled.txt
tests/fixtures/new_biomart.map
tests/fixtures/peptable.txt
tests/fixtures/peptable_db.sqlite
tests/fixtures/peptable_isoquant.txt
tests/fixtures/peptable_small.txt
tests/fixtures/peptides_trypsinized.yml
tests/fixtures/percolator_out.xml
tests/fixtures/pickfdr_assoc.txt
tests/fixtures/pickfdr_ensg.txt
tests/fixtures/proteins.fasta
tests/fixtures/protfdr.txt
tests/fixtures/prottable.txt
tests/fixtures/prottable_assoc.txt
tests/fixtures/prottable_assoc_db.sqlite
tests/fixtures/prottable_assoc_decoy.txt
tests/fixtures/prottable_assoc_target.txt
tests/fixtures/prottable_db.sqlite
tests/fixtures/prottable_decoy.txt
tests/fixtures/prottable_ensg_decoy.txt
tests/fixtures/prottable_ensg_target.txt
tests/fixtures/prottable_gene_db.sqlite
tests/fixtures/prottable_genes.txt
tests/fixtures/prottable_isoquant.txt
tests/fixtures/prottable_nopsm_db.sqlite
tests/fixtures/prottable_normalized_isoquant.txt
tests/fixtures/prottable_only_acc.txt
tests/fixtures/prottable_qvality.txt
tests/fixtures/prottable_ratio_isoquant.txt
tests/fixtures/prottable_target.txt
tests/fixtures/qvality.txt
tests/fixtures/rev_known_peptide_lookup.sqlite
tests/fixtures/spectra_lookup.sqlite
tests/fixtures/splitprotein_h0.xml
tests/fixtures/splitprotein_h1.xml
tests/fixtures/splittd_decoy_out.xml
tests/fixtures/splittd_target_out.xml
tests/fixtures/tmt_quant.consxml
tests/integration/__init__.py
tests/integration/basetests.py
tests/integration/mslookup_tests.py
tests/integration/mzidtsv_tests.py
tests/integration/peptable_tests.py
tests/integration/prottable_tests.py
tests/integration/pycolator_tests.py
tests/test_output/tmp15t5j2cm/built_protein_table.txt
tests/test_output/tmp31hmvtrf/built_protein_table.txt
tests/test_output/tmp4aqjgisr/built_protein_table.txt
tests/test_output/tmp5xxwl6m8/built_protein_table.txt
tests/test_output/tmp65dgadbe/built_protein_table.txt
tests/test_output/tmp8dgpkqrj/built_protein_table.txt
tests/test_output/tmp9alircyo/built_protein_table.txt
tests/test_output/tmp9p_ljbsa/built_protein_table.txt
tests/test_output/tmp_ggs35ph/built_protein_table.txt
tests/test_output/tmpacm5uky2/built_protein_table.txt
tests/test_output/tmpb647ufno/built_protein_table.txt
tests/test_output/tmpbr2v2_a8/built_protein_table.txt
tests/test_output/tmpcg420fh7/built_protein_table.txt
tests/test_output/tmpdhwkd2bq/built_protein_table.txt
tests/test_output/tmpdxw4ca9i/built_protein_table.txt
tests/test_output/tmph9lj6ouf/built_protein_table.txt
tests/test_output/tmphcaltic7/built_protein_table.txt
tests/test_output/tmpl78kjooz/built_protein_table.txt
tests/test_output/tmpm_crdjqg/built_protein_table.txt
tests/test_output/tmpmlcwxenh/built_protein_table.txt
tests/test_output/tmpnu7dv1ti/built_protein_table.txt
tests/test_output/tmpqf2jyorz/built_protein_table.txt
tests/test_output/tmpqv_03o5f/built_protein_table.txt
tests/test_output/tmprrtnu_en/built_protein_table.txt
tests/test_output/tmprsfpkh9l/built_protein_table.txt
tests/test_output/tmpzq023p06/built_protein_table.txt
tests/test_output/tmpzsxe_ltx/built_protein_table.txt
tests/test_output/tmpzyfcuel4/built_protein_table.txt