ursgal
dev
Introduction
Quick Start Tutorial
General Structure
UController
UNode
UCore
UMapMaster
Chemical Composition
Unimod Mapper
Ursgal Results
Ursgal Parameters
Available Search Engines
Converter Engines
Other Engines
Create/Implement your own UNode
Example Scripts
Changelog
Contribution Guidelines
Frequently Asked Questions
Known Issues
ursgal
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Index
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
_
__init__() (ursgal.UNode method)
__weakref__ (ursgal.UNode attribute)
_create_fcache() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
_execute() (ursgal.UNode method)
(ursgal.wrappers.combine_FDR_0_1.combine_FDR_0_1 method)
(ursgal.wrappers.combine_pep_1_0_0.combine_pep_1_0_0 method)
(ursgal.wrappers.csv2counted_results_1_0_0.csv2counted_results_1_0_0 method)
(ursgal.wrappers.csv2ssl_1_0_0.csv2ssl_1_0_0 method)
(ursgal.wrappers.filter_csv_1_0_0.filter_csv_1_0_0 method)
(ursgal.wrappers.generate_target_decoy_1_0_0.generate_target_decoy_1_0_0 method)
(ursgal.wrappers.get_ftp_files_1_0_0.get_ftp_files_1_0_0 method)
(ursgal.wrappers.get_http_files_1_0_0.get_http_files_1_0_0 method)
(ursgal.wrappers.merge_csvs_1_0_0.merge_csvs_1_0_0 method)
(ursgal.wrappers.sanitize_csv_1_0_0.sanitize_csv_1_0_0 method)
(ursgal.wrappers.sugarpy_plot_1_0_0.sugarpy_plot_1_0_0 method)
(ursgal.wrappers.sugarpy_run_1_0_0.sugarpy_run_1_0_0 method)
(ursgal.wrappers.unify_csv_1_0_0.unify_csv_1_0_0 method)
(ursgal.wrappers.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0 method)
(ursgal.wrappers.venndiagram_1_0_0.venndiagram_1_0_0 method)
_format_hit_dict() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
_group_psms() (ursgal.UNode method)
A
abs_paths_for_specific_keys() (ursgal.UNode method)
add_chemical_formula() (ursgal.ChemicalComposition method)
add_glycan() (ursgal.ChemicalComposition method)
add_peptide() (ursgal.ChemicalComposition method)
analyze() (in module cascade_search_example)
(in module grouped_search_example)
(in module machine_offset_bruderer_sweep)
(in module ungrouped_search_example)
appMass2element_list() (ursgal.UnimodMapper method)
appMass2id_list() (ursgal.UnimodMapper method)
appMass2name_list() (ursgal.UnimodMapper method)
B
build_lookup() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
build_lookup_from_file() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
C
cache_database() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v3 method)
(ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v4 method)
calc_md5() (ursgal.UNode method)
calculate_mass() (in module ursgal.ucore)
calculate_mz() (in module ursgal.ucore)
ChemicalComposition (class in ursgal)
clear() (ursgal.ChemicalComposition method)
collect_and_translate_params() (ursgal.UNode method)
combine_FDR_0_1 (class in ursgal.wrappers.combine_FDR_0_1)
combine_pep_1_0_0 (class in ursgal.wrappers.combine_pep_1_0_0)
combine_search_results() (ursgal.ucontroller.UController method)
compare_json_and_local_ursgal_version() (ursgal.UNode method)
composition2id_list() (ursgal.UnimodMapper method)
composition2mass() (ursgal.UnimodMapper method)
composition2name_list() (ursgal.UnimodMapper method)
composition_at_pos (ursgal.ChemicalComposition attribute)
composition_of_aa_at_pos (ursgal.ChemicalComposition attribute)
composition_of_mod_at_pos (ursgal.ChemicalComposition attribute)
convert() (ursgal.ucontroller.UController method)
convert_dalton_to_ppm() (in module ursgal.ucore)
convert_ppm_to_dalton() (in module ursgal.ucore)
convert_results_to_csv() (ursgal.ucontroller.UController method)
convert_to_mgf_and_update_rt_lookup() (ursgal.ucontroller.UController method)
count_distinct_psms() (in module ursgal.ucore)
csv2counted_results_1_0_0 (class in ursgal.wrappers.csv2counted_results_1_0_0)
csv2ssl_1_0_0 (class in ursgal.wrappers.csv2ssl_1_0_0)
D
deepnovo_0_0_1 (class in ursgal.wrappers.deepnovo_0_0_1)
deepnovo_pointnovo (class in ursgal.wrappers.deepnovo_pointnovo)
determine_availability_of_unodes() (ursgal.ucontroller.UController method)
determine_common_name() (ursgal.UNode method)
determine_common_top_level_folder() (ursgal.UNode method)
digest() (in module ursgal.ucore)
distinguish_multi_and_single_input() (ursgal.ucontroller.UController method)
download_resources() (ursgal.ucontroller.UController method)
dump_json_and_calc_md5() (ursgal.UNode method)
dump_multi_json() (ursgal.ucontroller.UController method)
E
engine_sanity_check() (ursgal.ucontroller.UController method)
eval_if_run_needs_to_be_executed() (ursgal.ucontroller.UController method)
execute_misc_engine() (ursgal.ucontroller.UController method)
execute_unode() (ursgal.ucontroller.UController method)
F
fetch_file() (ursgal.ucontroller.UController method)
filter_csv() (ursgal.ucontroller.UController method)
filter_csv_1_0_0 (class in ursgal.wrappers.filter_csv_1_0_0)
fix_md5_and_file_in_json() (ursgal.UNode method)
flash_lfq_1_1_1 (class in ursgal.wrappers.flash_lfq_1_1_1)
flatten_list() (ursgal.UNode method)
format_templates() (ursgal.wrappers.kojak_1_5_3.kojak_1_5_3 method)
(ursgal.wrappers.xtandem_piledriver.xtandem_piledriver method)
(ursgal.wrappers.xtandem_sledgehammer.xtandem_sledgehammer method)
(ursgal.wrappers.xtandem_vengeance.xtandem_vengeance method)
G
generate_multi_file_dicts() (ursgal.ucontroller.UController method)
generate_multi_helper_file() (ursgal.ucontroller.UController method)
generate_target_decoy() (ursgal.ucontroller.UController method)
generate_target_decoy_1_0_0 (class in ursgal.wrappers.generate_target_decoy_1_0_0)
get_ftp_files_1_0_0 (class in ursgal.wrappers.get_ftp_files_1_0_0)
get_http_files_1_0_0 (class in ursgal.wrappers.get_http_files_1_0_0)
get_last_engine() (ursgal.UNode method)
get_last_engine_type() (ursgal.UNode method)
get_last_search_engine() (ursgal.UNode method)
get_masked_params() (ursgal.umapmaster.UParamMapper method)
get_mzml_that_corresponds_to_mgf() (ursgal.ucontroller.UController method)
group_styles() (ursgal.umapmaster.UParamMapper method)
guess_engine_name() (ursgal.ucontroller.UController method)
H
hill_notation() (ursgal.ChemicalComposition method)
hill_notation_unimod() (ursgal.ChemicalComposition method)
I
id2composition() (ursgal.UnimodMapper method)
id2mass() (ursgal.UnimodMapper method)
id2name() (ursgal.UnimodMapper method)
import_engine_as_python_function() (ursgal.UNode method)
input_file_sanity_check() (ursgal.ucontroller.UController method)
K
kojak_1_5_3 (class in ursgal.wrappers.kojak_1_5_3)
kojak_percolator_2_08 (class in ursgal.wrappers.kojak_percolator_2_08)
M
main() (in module barth_et_al_large_scale)
(in module bsa_fragment_mass_tolerance_example)
(in module bsa_ppm_offset_test)
(in module bsa_precursor_mass_tolerance_example)
(in module complete_chlamydomonas_proteome_match)
(in module complete_proteome_match)
(in module convert_raw_to_mzml)
(in module do_it_all_folder_wide)
(in module example_pglyco_workflow)
,
[1]
,
[2]
(in module filter_csv_for_mods_example)
(in module filter_csv_validation_example)
(in module human_br_complete_workflow)
(in module mgf_conversion_inside_and_outside_loop)
(in module msgf_version_comparison)
(in module open_modification_search_incl_combined_pep)
(in module ptmshepherd_mass_difference_processing)
(in module sanitize_combined_results)
(in module search_with_label_15N)
(in module simple_combined_fdr_score)
(in module simple_de_novo_search)
(in module simple_example_search)
(in module simple_mgf_conversion)
(in module simple_venn_example)
(in module sugarpy_example_workflow)
(in module sugarpy_plot_annotated_specs)
(in module target_decoy_generation_example)
(in module test_node_execution)
(in module ursgal.resources.platform_independent.arc_independent.csv2counted_results_1_0_0.csv2counted_results_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.csv2ssl_1_0_0.csv2ssl_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.filter_csv_1_0_0.filter_csv_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.generate_target_decoy_1_0_0.generate_target_decoy_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.get_ftp_files_1_0_0.get_ftp_files_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.get_http_files_1_0_0.get_http_files_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.mascot_dat2csv_1_0_0.mascot_dat2csv_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.merge_csvs_1_0_0.merge_csvs_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.mzml2mgf_2_0_0.mzml2mgf_2_0_0)
(in module ursgal.resources.platform_independent.arc_independent.pyqms_1_0_0.pyqms_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.sanitize_csv_1_0_0.sanitize_csv_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.unify_csv_1_0_0.unify_csv_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.venndiagram_1_0_0.venndiagram_1_0_0)
(in module ursgal.resources.platform_independent.arc_independent.xtandem2csv_1_0_0.xtandem2csv_1_0_0)
(in module xtandem_version_comparison)
(in module xtandem_version_comparison_qexactive)
map_mods() (ursgal.UNode method)
map_peptide() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
map_peptides() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
(ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v3 method)
(ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v4 method)
map_peptides_to_fasta() (ursgal.ucontroller.UController method)
mapping_dicts() (ursgal.umapmaster.UParamMapper method)
mascot_dat2csv_1_0_0 (class in ursgal.wrappers.mascot_dat2csv_1_0_0)
mass2composition_list() (ursgal.UnimodMapper method)
mass2id_list() (ursgal.UnimodMapper method)
mass2name_list() (ursgal.UnimodMapper method)
merge_csvs() (ursgal.ucontroller.UController method)
merge_csvs_1_0_0 (class in ursgal.wrappers.merge_csvs_1_0_0)
merge_duplicate_psm_rows() (in module ursgal.ucore)
merge_rowdicts() (in module ursgal.ucore)
moda_v1_51 (class in ursgal.wrappers.moda_v1_51)
moda_v1_61 (class in ursgal.wrappers.moda_v1_61)
moda_v1_62 (class in ursgal.wrappers.moda_v1_62)
msamanda_1_0_0_5242 (class in ursgal.wrappers.msamanda_1_0_0_5242)
msamanda_1_0_0_5243 (class in ursgal.wrappers.msamanda_1_0_0_5243)
msamanda_1_0_0_7503 (class in ursgal.wrappers.msamanda_1_0_0_7503)
msamanda_1_0_0_7504 (class in ursgal.wrappers.msamanda_1_0_0_7504)
msamanda_2_0_0_10695 (class in ursgal.wrappers.msamanda_2_0_0_10695)
msamanda_2_0_0_11219 (class in ursgal.wrappers.msamanda_2_0_0_11219)
msamanda_2_0_0_13723 (class in ursgal.wrappers.msamanda_2_0_0_13723)
msamanda_2_0_0_14665 (class in ursgal.wrappers.msamanda_2_0_0_14665)
msamanda_2_0_0_9695 (class in ursgal.wrappers.msamanda_2_0_0_9695)
msamanda_2_0_0_9706 (class in ursgal.wrappers.msamanda_2_0_0_9706)
msfragger_20170103 (class in ursgal.wrappers.msfragger_20170103)
msfragger_20171106 (class in ursgal.wrappers.msfragger_20171106)
msfragger_20190222 (class in ursgal.wrappers.msfragger_20190222)
msfragger_20190628 (class in ursgal.wrappers.msfragger_20190628)
msfragger_2_3 (class in ursgal.wrappers.msfragger_2_3)
msfragger_3_0 (class in ursgal.wrappers.msfragger_3_0)
msgfplus2csv_py_v1_0_0 (class in ursgal.wrappers.msgfplus2csv_py_v1_0_0)
msgfplus2csv_v1_2_0 (class in ursgal.wrappers.msgfplus2csv_v1_2_0)
msgfplus2csv_v1_2_1 (class in ursgal.wrappers.msgfplus2csv_v1_2_1)
msgfplus2csv_v2016_09_16 (class in ursgal.wrappers.msgfplus2csv_v2016_09_16)
msgfplus2csv_v2017_01_27 (class in ursgal.wrappers.msgfplus2csv_v2017_01_27)
msgfplus2csv_v2017_07_04 (class in ursgal.wrappers.msgfplus2csv_v2017_07_04)
msgfplus_v2016_09_16 (class in ursgal.wrappers.msgfplus_v2016_09_16)
msgfplus_v2017_01_27 (class in ursgal.wrappers.msgfplus_v2017_01_27)
msgfplus_v2018_01_30 (class in ursgal.wrappers.msgfplus_v2018_01_30)
msgfplus_v2018_06_28 (class in ursgal.wrappers.msgfplus_v2018_06_28)
msgfplus_v2018_09_12 (class in ursgal.wrappers.msgfplus_v2018_09_12)
msgfplus_v2019_01_22 (class in ursgal.wrappers.msgfplus_v2019_01_22)
msgfplus_v2019_04_18 (class in ursgal.wrappers.msgfplus_v2019_04_18)
msgfplus_v2019_07_03 (class in ursgal.wrappers.msgfplus_v2019_07_03)
msgfplus_v9979 (class in ursgal.wrappers.msgfplus_v9979)
myrimatch_2_1_138 (class in ursgal.wrappers.myrimatch_2_1_138)
myrimatch_2_2_140 (class in ursgal.wrappers.myrimatch_2_2_140)
mzidentml_lib_1_6_10 (class in ursgal.wrappers.mzidentml_lib_1_6_10)
mzidentml_lib_1_6_11 (class in ursgal.wrappers.mzidentml_lib_1_6_11)
mzidentml_lib_1_7 (class in ursgal.wrappers.mzidentml_lib_1_7)
mzml2mgf_1_0_0 (class in ursgal.wrappers.mzml2mgf_1_0_0)
mzml2mgf_2_0_0 (class in ursgal.wrappers.mzml2mgf_2_0_0)
N
name2composition() (ursgal.UnimodMapper method)
name2id() (ursgal.UnimodMapper method)
name2mass() (ursgal.UnimodMapper method)
novor_1_05 (class in ursgal.wrappers.novor_1_05)
novor_1_1beta (class in ursgal.wrappers.novor_1_1beta)
O
omssa_2_1_9 (class in ursgal.wrappers.omssa_2_1_9)
P
parse_fasta() (in module ursgal.ucore)
pepnovo_3_1 (class in ursgal.wrappers.pepnovo_3_1)
peptide_regex() (ursgal.UNode method)
percolator_2_08 (class in ursgal.wrappers.percolator_2_08)
percolator_3_2_1 (class in ursgal.wrappers.percolator_3_2_1)
percolator_3_4_0 (class in ursgal.wrappers.percolator_3_4_0)
pglyco_db_2_2_0 (class in ursgal.wrappers.pglyco_db_2_2_0)
pglyco_db_2_2_2 (class in ursgal.wrappers.pglyco_db_2_2_2)
pglyco_fdr_2_2_0 (class in ursgal.wrappers.pglyco_fdr_2_2_0)
pipi_1_4_5 (class in ursgal.wrappers.pipi_1_4_5)
pipi_1_4_6 (class in ursgal.wrappers.pipi_1_4_6)
plot_pygcluster_heatmap_from_csv_1_0_0 (class in ursgal.wrappers.plot_pygcluster_heatmap_from_csv_1_0_0)
pnovo_3_1_3 (class in ursgal.wrappers.pnovo_3_1_3)
postflight() (ursgal.UNode method)
(ursgal.wrappers.deepnovo_0_0_1.deepnovo_0_0_1 method)
(ursgal.wrappers.deepnovo_pointnovo.deepnovo_pointnovo method)
(ursgal.wrappers.flash_lfq_1_1_1.flash_lfq_1_1_1 method)
(ursgal.wrappers.kojak_1_5_3.kojak_1_5_3 method)
(ursgal.wrappers.kojak_percolator_2_08.kojak_percolator_2_08 method)
(ursgal.wrappers.moda_v1_51.moda_v1_51 method)
(ursgal.wrappers.moda_v1_61.moda_v1_61 method)
(ursgal.wrappers.moda_v1_62.moda_v1_62 method)
(ursgal.wrappers.msamanda_1_0_0_5243.msamanda_1_0_0_5243 method)
(ursgal.wrappers.msamanda_2_0_0_9695.msamanda_2_0_0_9695 method)
(ursgal.wrappers.msfragger_20170103.msfragger_20170103 method)
(ursgal.wrappers.msfragger_20190628.msfragger_20190628 method)
(ursgal.wrappers.msfragger_3_0.msfragger_3_0 method)
(ursgal.wrappers.msgfplus2csv_v1_2_1.msgfplus2csv_v1_2_1 method)
(ursgal.wrappers.msgfplus2csv_v2016_09_16.msgfplus2csv_v2016_09_16 method)
(ursgal.wrappers.msgfplus2csv_v2017_07_04.msgfplus2csv_v2017_07_04 method)
(ursgal.wrappers.msgfplus_v2016_09_16.msgfplus_v2016_09_16 method)
(ursgal.wrappers.msgfplus_v2019_07_03.msgfplus_v2019_07_03 method)
(ursgal.wrappers.myrimatch_2_1_138.myrimatch_2_1_138 method)
(ursgal.wrappers.novor_1_05.novor_1_05 method)
(ursgal.wrappers.novor_1_1beta.novor_1_1beta method)
(ursgal.wrappers.omssa_2_1_9.omssa_2_1_9 method)
(ursgal.wrappers.pepnovo_3_1.pepnovo_3_1 method)
(ursgal.wrappers.percolator_2_08.percolator_2_08 method)
(ursgal.wrappers.percolator_3_2_1.percolator_3_2_1 method)
(ursgal.wrappers.pglyco_db_2_2_0.pglyco_db_2_2_0 method)
(ursgal.wrappers.pglyco_fdr_2_2_0.pglyco_fdr_2_2_0 method)
(ursgal.wrappers.pipi_1_4_5.pipi_1_4_5 method)
(ursgal.wrappers.pnovo_3_1_3.pnovo_3_1_3 method)
(ursgal.wrappers.pparse_2_0.pparse_2_0 method)
(ursgal.wrappers.ptminer_1_0.ptminer_1_0 method)
(ursgal.wrappers.ptmshepherd_0_3_5.ptmshepherd_0_3_5 method)
(ursgal.wrappers.qvality_2_02.qvality_2_02 method)
(ursgal.wrappers.tag_graph_1_8_0.tag_graph_1_8_0 method)
(ursgal.wrappers.xtandem_piledriver.xtandem_piledriver method)
(ursgal.wrappers.xtandem_sledgehammer.xtandem_sledgehammer method)
(ursgal.wrappers.xtandem_vengeance.xtandem_vengeance method)
pparse_2_0 (class in ursgal.wrappers.pparse_2_0)
preflight() (ursgal.UNode method)
(ursgal.wrappers.combine_FDR_0_1.combine_FDR_0_1 method)
(ursgal.wrappers.combine_pep_1_0_0.combine_pep_1_0_0 method)
(ursgal.wrappers.deepnovo_0_0_1.deepnovo_0_0_1 method)
(ursgal.wrappers.deepnovo_pointnovo.deepnovo_pointnovo method)
(ursgal.wrappers.flash_lfq_1_1_1.flash_lfq_1_1_1 method)
(ursgal.wrappers.kojak_1_5_3.kojak_1_5_3 method)
(ursgal.wrappers.kojak_percolator_2_08.kojak_percolator_2_08 method)
(ursgal.wrappers.moda_v1_51.moda_v1_51 method)
(ursgal.wrappers.moda_v1_61.moda_v1_61 method)
(ursgal.wrappers.moda_v1_62.moda_v1_62 method)
(ursgal.wrappers.msamanda_1_0_0_5243.msamanda_1_0_0_5243 method)
(ursgal.wrappers.msamanda_2_0_0_9695.msamanda_2_0_0_9695 method)
(ursgal.wrappers.msfragger_20170103.msfragger_20170103 method)
(ursgal.wrappers.msfragger_20190628.msfragger_20190628 method)
(ursgal.wrappers.msfragger_3_0.msfragger_3_0 method)
(ursgal.wrappers.msgfplus2csv_v1_2_1.msgfplus2csv_v1_2_1 method)
(ursgal.wrappers.msgfplus2csv_v2016_09_16.msgfplus2csv_v2016_09_16 method)
(ursgal.wrappers.msgfplus2csv_v2017_07_04.msgfplus2csv_v2017_07_04 method)
(ursgal.wrappers.msgfplus_v2016_09_16.msgfplus_v2016_09_16 method)
(ursgal.wrappers.msgfplus_v2019_07_03.msgfplus_v2019_07_03 method)
(ursgal.wrappers.msgfplus_v9979.msgfplus_v9979 method)
(ursgal.wrappers.myrimatch_2_1_138.myrimatch_2_1_138 method)
(ursgal.wrappers.mzidentml_lib_1_6_10.mzidentml_lib_1_6_10 method)
(ursgal.wrappers.novor_1_05.novor_1_05 method)
(ursgal.wrappers.novor_1_1beta.novor_1_1beta method)
(ursgal.wrappers.omssa_2_1_9.omssa_2_1_9 method)
(ursgal.wrappers.pepnovo_3_1.pepnovo_3_1 method)
(ursgal.wrappers.percolator_2_08.percolator_2_08 method)
(ursgal.wrappers.percolator_3_2_1.percolator_3_2_1 method)
(ursgal.wrappers.pglyco_db_2_2_0.pglyco_db_2_2_0 method)
(ursgal.wrappers.pglyco_fdr_2_2_0.pglyco_fdr_2_2_0 method)
(ursgal.wrappers.pipi_1_4_5.pipi_1_4_5 method)
(ursgal.wrappers.pnovo_3_1_3.pnovo_3_1_3 method)
(ursgal.wrappers.pparse_2_0.pparse_2_0 method)
(ursgal.wrappers.ptminer_1_0.ptminer_1_0 method)
(ursgal.wrappers.ptmshepherd_0_3_5.ptmshepherd_0_3_5 method)
(ursgal.wrappers.qvality_2_02.qvality_2_02 method)
(ursgal.wrappers.tag_graph_1_8_0.tag_graph_1_8_0 method)
(ursgal.wrappers.thermo_raw_file_parser_1_1_2.thermo_raw_file_parser_1_1_2 method)
(ursgal.wrappers.xtandem_piledriver.xtandem_piledriver method)
(ursgal.wrappers.xtandem_sledgehammer.xtandem_sledgehammer method)
(ursgal.wrappers.xtandem_vengeance.xtandem_vengeance method)
print_current_params() (in module ursgal.ucore)
ptminer_1_0 (class in ursgal.wrappers.ptminer_1_0)
ptmshepherd_0_3_5 (class in ursgal.wrappers.ptmshepherd_0_3_5)
purge_fasta_info() (ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v2 method)
(ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0.UPeptideMapper_v3 method)
Q
quantify() (ursgal.ucontroller.UController method)
qvality_2_02 (class in ursgal.wrappers.qvality_2_02)
R
raw2mzid() (ursgal.wrappers.mzidentml_lib_1_6_10.mzidentml_lib_1_6_10 method)
reformat_peptide() (in module ursgal.ucore)
run() (ursgal.UNode method)
run_unode_if_required() (ursgal.ucontroller.UController method)
S
sanitize_csv_1_0_0 (class in ursgal.wrappers.sanitize_csv_1_0_0)
sanitize_userdefined_output_filename() (ursgal.ucontroller.UController method)
search() (in module cascade_search_example)
(in module grouped_search_example)
(in module machine_offset_bruderer_sweep)
(in module ungrouped_search_example)
(ursgal.ucontroller.UController method)
search_mgf() (ursgal.ucontroller.UController method)
set_file_info_dict() (ursgal.ucontroller.UController method)
set_profile() (ursgal.ucontroller.UController method)
show_unode_overview() (ursgal.ucontroller.UController method)
subtract_chemical_formula() (ursgal.ChemicalComposition method)
subtract_peptide() (ursgal.ChemicalComposition method)
sugarpy_plot_1_0_0 (class in ursgal.wrappers.sugarpy_plot_1_0_0)
sugarpy_run_1_0_0 (class in ursgal.wrappers.sugarpy_run_1_0_0)
T
tag_graph_1_8_0 (class in ursgal.wrappers.tag_graph_1_8_0)
terminal_supports_color() (in module ursgal.ucore)
thermo_raw_file_parser_1_1_2 (class in ursgal.wrappers.thermo_raw_file_parser_1_1_2)
time_point() (ursgal.UNode method)
U
UController (class in ursgal.ucontroller)
unify_csv() (ursgal.ucontroller.UController method)
unify_csv_1_0_0 (class in ursgal.wrappers.unify_csv_1_0_0)
UnimodMapper (class in ursgal)
UNode (class in ursgal)
UParamMapper (class in ursgal.umapmaster)
update_output_json() (ursgal.UNode method)
update_params_with_io_data() (ursgal.UNode method)
upeptide_mapper_1_0_0 (class in ursgal.wrappers.upeptide_mapper_1_0_0)
UPeptideMapper_v2 (class in ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0)
UPeptideMapper_v3 (class in ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0)
UPeptideMapper_v4 (class in ursgal.resources.platform_independent.arc_independent.upeptide_mapper_1_0_0.upeptide_mapper_1_0_0)
ursgal.ucore (module)
use() (ursgal.ChemicalComposition method)
V
validate() (ursgal.ucontroller.UController method)
venndiagram_1_0_0 (class in ursgal.wrappers.venndiagram_1_0_0)
verify_engine_produced_an_output_file() (ursgal.ucontroller.UController method)
visualize() (ursgal.ucontroller.UController method)
W
write_input_tsv() (ursgal.wrappers.ptmshepherd_0_3_5.ptmshepherd_0_3_5 method)
write_param_file() (ursgal.wrappers.myrimatch_2_1_138.myrimatch_2_1_138 method)
writeXML() (ursgal.UnimodMapper method)
X
xtandem2csv_1_0_0 (class in ursgal.wrappers.xtandem2csv_1_0_0)
xtandem_alanine (class in ursgal.wrappers.xtandem_alanine)
xtandem_cyclone_2010 (class in ursgal.wrappers.xtandem_cyclone_2010)
xtandem_jackhammer (class in ursgal.wrappers.xtandem_jackhammer)
xtandem_piledriver (class in ursgal.wrappers.xtandem_piledriver)
xtandem_sledgehammer (class in ursgal.wrappers.xtandem_sledgehammer)
xtandem_vengeance (class in ursgal.wrappers.xtandem_vengeance)
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