AUTHORS.txt
COPYING.txt
MANIFEST.in
README.rst
requirements.txt
setup.cfg
setup.py
example_data/BSA.fasta
example_data/BSA1.mzML
example_data/misc/filter_csv_for_mods_example_omssa_2_1_9_pmap_unified.csv
example_data/misc/filter_csv_for_mods_example_omssa_2_1_9_pmap_unified_percolator_2_08_validated.csv
example_data/misc/heatmap_example_input.csv
example_scripts/barth_et_al_large_scale.py
example_scripts/bsa_fragment_mass_tolerance_example.py
example_scripts/bsa_ppm_offset_test.py
example_scripts/bsa_precursor_mass_tolerance_example.py
example_scripts/cascade_search_example.py
example_scripts/compare_engine_search_speed.py
example_scripts/compare_mzIdentML_converter_versions.py
example_scripts/compare_percolator_versions.py
example_scripts/complete_chlamydomonas_proteome_match.py
example_scripts/complete_proteome_match.py
example_scripts/convert_raw_to_mzml.py
example_scripts/do_it_all_folder_wide.py
example_scripts/filter_csv_for_mods_example.py
example_scripts/filter_csv_validation_example.py
example_scripts/generate_target_decoy_from_fasta.py
example_scripts/get_file_from_ftp_server_example.py
example_scripts/grouped_search_example.py
example_scripts/human_br_complete_workflow.py
example_scripts/machine_offset_bruderer_sweep.py
example_scripts/map_peptides_to_fasta_comparison.py
example_scripts/mgf_conversion_inside_and_outside_loop.py
example_scripts/msgf_plus_version_comparison_qexactive.py
example_scripts/msgf_version_comparison.py
example_scripts/quantify_JB_example.py
example_scripts/search_and_conversion_to_ssl.py
example_scripts/search_with_label_15N.py
example_scripts/show_unode_paramters.py
example_scripts/simple_combined_fdr_score.py
example_scripts/simple_crosslink_search.py
example_scripts/simple_de_novo_search.py
example_scripts/simple_example_pglyco_workflow.py
example_scripts/simple_example_search.py
example_scripts/simple_heatmap_example.py
example_scripts/simple_mgf_conversion.py
example_scripts/simple_venn_example.py
example_scripts/svm_post_processing_folder_wide.py
example_scripts/target_decoy_generation_example.py
example_scripts/test_node_execution.py
example_scripts/ungrouped_search_example.py
example_scripts/unify_mascot_dat.py
example_scripts/validate_upeptide_mapper_v3_vs_v4.py
example_scripts/xtandem_version_comparison.py
example_scripts/xtandem_version_comparison_qexactive.py
tests/ChemicalComposition_tests.py
tests/UnimodMapper_test.py
tests/calc_md5_test.py
tests/cc_calculate_mass_test.py
tests/chk_format_node_param_test.py
tests/complete_search_with_omssa_test.py
tests/csv2counted_results_test.py
tests/csv2ssl_test.py
tests/determine_common_head_tail_part_of_names_test.py
tests/determine_common_top_level_folder_test.py
tests/digest_test.py
tests/distinguish_multi_and_single_input_test.py
tests/filter_csv_test.py
tests/map_mods_test.py
tests/merge_colnames_multiple_values_test.py
tests/merge_duplicate_rows_test.py
tests/merge_fdicts_test.py
tests/norm_paths_for_specific_params_keys_test.py
tests/omssa_to_unimod_correction_test.py
tests/peptide_regex_test.py
tests/reformat_peptide_test.py
tests/reset_controller_test.py
tests/sanitize_userdefined_output_filename_test.py
tests/sliding_window_test.py
tests/stepwise_search_with_omssa_test.py
tests/translate_params_test.py
tests/umapmaster_test.py
tests/unify_msamanda_csv_test.py
tests/unify_msfragger_csv_test.py
tests/unify_msgfplus_csv_test.py
tests/unify_myrimatch_csv_test.py
tests/unify_novor_csv_test.py
tests/unify_nterminal_test.py
tests/unify_omssa_csv_test.py
tests/unify_pipi_csv_test.py
tests/unify_xtandem_csv_test.py
tests/upeptide_mapper_node_test.py
tests/upeptide_mapper_v2_test.py
tests/upeptide_mapper_v3_test.py
tests/venndiagram_test.py
tests/xtandem2csv_test.py
tests/data/BSA.fasta
tests/data/TMT_msgfplus_pmap.csv
tests/data/TMT_msgfplus_pmap_unified.csv_expected.csv
tests/data/TMT_xtandem_vengeance_pmap.csv
tests/data/TMT_xtandem_vengeance_pmap_unified.csv_expected.csv
tests/data/Test.fasta
tests/data/_test_ursgal_lookup.pkl
tests/data/test.json
tests/data/test_BSA1_omssa_2_1_9_unified_filter_csv_test.csv
tests/data/test_Creinhardtii_QE_pH11.mzML
tests/data/test_Creinhardtii_QE_pH8.mzML
tests/data/test_Creinhardtii_target_decoy.fasta
tests/data/test_merge_duplicate_rows.csv
tests/data/test_merge_duplicate_rows_expected.csv
tests/data/test_shipped_Creinhardtii_QE_pH8_omssa_2_1_9_unified.csv
tests/data/test_upeptide_mapper.csv
tests/data/test_without_database.json
tests/data/omssa_2_1_9/BSA1_omssa_2_1_9.csv
tests/data/omssa_2_1_9/test_BSA1_omssa_2_1_9.csv
tests/data/xtandem_sledgehammer/test_BSA1_xtandem.csv
tests/data/xtandem_sledgehammer/test_BSA1_xtandem.xml
tests/data/xtandem_sledgehammer/test_BSA1_xtandem_expected.csv
tests/data/xtandem_sledgehammer/test_BSA1_xtandem_sledgehammer.csv
ursgal/__init__.py
ursgal/chemical_composition.py
ursgal/chemical_composition_kb.py
ursgal/profiles.py
ursgal/ucontroller.py
ursgal/ucore.py
ursgal/ukb.py
ursgal/umapmaster.py
ursgal/unimod_mapper.py
ursgal/unode.py
ursgal/uparams.py
ursgal/version.txt
ursgal.egg-info/PKG-INFO
ursgal.egg-info/SOURCES.txt
ursgal.egg-info/dependency_links.txt
ursgal.egg-info/requires.txt
ursgal.egg-info/top_level.txt
ursgal/resources/platform_independent/arc_independent/_test_node/test_node.py
ursgal/resources/platform_independent/arc_independent/add_estimated_fdr_1_0_0/add_estimated_fdr_1_0_0.py
ursgal/resources/platform_independent/arc_independent/combine_FDR_0_1/combine_FDR_0_1.py
ursgal/resources/platform_independent/arc_independent/combine_pep_1_0_0/combine_pep_1_0_0.py
ursgal/resources/platform_independent/arc_independent/csv2counted_results_1_0_0/csv2counted_results_1_0_0.py
ursgal/resources/platform_independent/arc_independent/csv2ssl_1_0_0/csv2ssl_1_0_0.py
ursgal/resources/platform_independent/arc_independent/ext/unimod.xml
ursgal/resources/platform_independent/arc_independent/filter_csv_1_0_0/filter_csv_1_0_0.py
ursgal/resources/platform_independent/arc_independent/generate_target_decoy_1_0_0/generate_target_decoy_1_0_0.py
ursgal/resources/platform_independent/arc_independent/get_ftp_files_1_0_0/get_ftp_files_1_0_0.py
ursgal/resources/platform_independent/arc_independent/get_http_files_1_0_0/get_http_files_1_0_0.py
ursgal/resources/platform_independent/arc_independent/mascot_dat2csv_1_0_0/mascot_dat2csv_1_0_0.py
ursgal/resources/platform_independent/arc_independent/merge_csvs_1_0_0/merge_csvs_1_0_0.py
ursgal/resources/platform_independent/arc_independent/mgf_to_rt_lookup_1_0_0/mgf_to_rt_lookup_1_0_0.py
ursgal/resources/platform_independent/arc_independent/msgfplus2csv_py_v1_0_0/msgfplus2csv_py_v1_0_0.py
ursgal/resources/platform_independent/arc_independent/mzml2dta_0_1_0/mzml2dta_0_1_0.py
ursgal/resources/platform_independent/arc_independent/mzml2mgf_1_0_0/mzml2mgf_1_0_0.py
ursgal/resources/platform_independent/arc_independent/mzml2mgf_2_0_0/mzml2mgf_2_0_0.py
ursgal/resources/platform_independent/arc_independent/naive_bayes_1_0_0/naive_bayes_1_0_0.py
ursgal/resources/platform_independent/arc_independent/plot_pygcluster_heatmap_from_csv_1_0_0/plot_pygcluster_heatmap_from_csv_1_0_0.py
ursgal/resources/platform_independent/arc_independent/pyqms_1_0_0/pyqms_1_0_0.py
ursgal/resources/platform_independent/arc_independent/sanitize_csv_1_0_0/sanitize_csv_1_0_0.py
ursgal/resources/platform_independent/arc_independent/svm_1_0_0/misc.py
ursgal/resources/platform_independent/arc_independent/svm_1_0_0/svm_1_0_0.py
ursgal/resources/platform_independent/arc_independent/unify_csv_1_0_0/unify_csv_1_0_0.py
ursgal/resources/platform_independent/arc_independent/upeptide_mapper_1_0_0/proposed_changes.py
ursgal/resources/platform_independent/arc_independent/upeptide_mapper_1_0_0/upeptide_mapper_1_0_0.py
ursgal/resources/platform_independent/arc_independent/venndiagram_1_0_0/venndiagram_1_0_0.py
ursgal/resources/platform_independent/arc_independent/venndiagram_1_1_0/venndiagram_1_1_0.py
ursgal/resources/platform_independent/arc_independent/xtandem2csv_1_0_0/xtandem2csv_1_0_0.py
ursgal/wrappers/_test_node.py
ursgal/wrappers/add_estimated_fdr_1_0_0.py
ursgal/wrappers/combine_FDR_0_1.py
ursgal/wrappers/combine_pep_1_0_0.py
ursgal/wrappers/comet_2014_02_rev_2.py
ursgal/wrappers/compomics_utilities_4_11_5.py
ursgal/wrappers/crux_2_1.py
ursgal/wrappers/csv2counted_results_1_0_0.py
ursgal/wrappers/csv2ssl_1_0_0.py
ursgal/wrappers/deepnovo_0_0_1.py
ursgal/wrappers/filter_csv_1_0_0.py
ursgal/wrappers/generate_target_decoy_1_0_0.py
ursgal/wrappers/get_ftp_files_1_0_0.py
ursgal/wrappers/get_http_files_1_0_0.py
ursgal/wrappers/kojak_1_5_3.py
ursgal/wrappers/kojak_percolator_2_08.py
ursgal/wrappers/mascot_dat2csv_1_0_0.py
ursgal/wrappers/mascot_x_x_x.py
ursgal/wrappers/merge_csvs_1_0_0.py
ursgal/wrappers/mgf_to_rt_lookup_1_0_0.py
ursgal/wrappers/moda_v1_51.py
ursgal/wrappers/moda_v1_61.py
ursgal/wrappers/moda_v1_62.py
ursgal/wrappers/msamanda_1_0_0_5242.py
ursgal/wrappers/msamanda_1_0_0_5243.py
ursgal/wrappers/msamanda_1_0_0_6299.py
ursgal/wrappers/msamanda_1_0_0_6300.py
ursgal/wrappers/msamanda_1_0_0_7503.py
ursgal/wrappers/msamanda_1_0_0_7504.py
ursgal/wrappers/msamanda_2_0_0_10695.py
ursgal/wrappers/msamanda_2_0_0_11219.py
ursgal/wrappers/msamanda_2_0_0_13723.py
ursgal/wrappers/msamanda_2_0_0_9695.py
ursgal/wrappers/msamanda_2_0_0_9706.py
ursgal/wrappers/msblender_09_2015.py
ursgal/wrappers/msfragger_20170103.py
ursgal/wrappers/msfragger_20171106.py
ursgal/wrappers/msfragger_20190222.py
ursgal/wrappers/msgfplus2csv_py_v1_0_0.py
ursgal/wrappers/msgfplus2csv_v1_2_0.py
ursgal/wrappers/msgfplus2csv_v1_2_1.py
ursgal/wrappers/msgfplus2csv_v2016_09_16.py
ursgal/wrappers/msgfplus2csv_v2017_01_27.py
ursgal/wrappers/msgfplus2csv_v2017_07_04.py
ursgal/wrappers/msgfplus_v2016_09_16.py
ursgal/wrappers/msgfplus_v2017_01_27.py
ursgal/wrappers/msgfplus_v2018_01_30.py
ursgal/wrappers/msgfplus_v2018_06_28.py
ursgal/wrappers/msgfplus_v2018_09_12.py
ursgal/wrappers/msgfplus_v2019_01_22.py
ursgal/wrappers/msgfplus_v2019_04_18.py
ursgal/wrappers/msgfplus_v9979.py
ursgal/wrappers/myrimatch_2_1_138.py
ursgal/wrappers/myrimatch_2_2_140.py
ursgal/wrappers/mzidentml_lib_1_6_10.py
ursgal/wrappers/mzidentml_lib_1_6_11.py
ursgal/wrappers/mzidentml_lib_1_7.py
ursgal/wrappers/mzml2mgf_1_0_0.py
ursgal/wrappers/mzml2mgf_2_0_0.py
ursgal/wrappers/naive_bayes_1_0_0.py
ursgal/wrappers/novor_1_05.py
ursgal/wrappers/novor_1_1beta.py
ursgal/wrappers/omssa_2_1_9.py
ursgal/wrappers/pepnovo_3_1.py
ursgal/wrappers/percolator_2_08.py
ursgal/wrappers/percolator_3_2_1.py
ursgal/wrappers/percolator_3_4_0.py
ursgal/wrappers/pglyco_db_2_2_0.py
ursgal/wrappers/pglyco_fdr_2_2_0.py
ursgal/wrappers/pipi_1_4_5.py
ursgal/wrappers/pipi_1_4_6.py
ursgal/wrappers/plot_pygcluster_heatmap_from_csv_1_0_0.py
ursgal/wrappers/pparse_2_0.py
ursgal/wrappers/pyqms_1_0_0.py
ursgal/wrappers/quameter_1_1_10165.py
ursgal/wrappers/qvality_2_02.py
ursgal/wrappers/sanitize_csv_1_0_0.py
ursgal/wrappers/sugarpy_plot_1_0_0.py
ursgal/wrappers/sugarpy_run_1_0_0.py
ursgal/wrappers/svm_1_0_0.py
ursgal/wrappers/thermo_raw_file_parser_1_1_2.py
ursgal/wrappers/unify_csv_1_0_0.py
ursgal/wrappers/uninovo_alpha_052013.py
ursgal/wrappers/upeptide_mapper_1_0_0.py
ursgal/wrappers/venndiagram_1_0_0.py
ursgal/wrappers/venndiagram_1_1_0.py
ursgal/wrappers/xtandem2csv_1_0_0.py
ursgal/wrappers/xtandem_alanine.py
ursgal/wrappers/xtandem_cyclone_2010.py
ursgal/wrappers/xtandem_jackhammer.py
ursgal/wrappers/xtandem_piledriver.py
ursgal/wrappers/xtandem_sledgehammer.py
ursgal/wrappers/xtandem_vengeance.py