| Previous changeset 29:78fad25eff17 (2016-06-10) Next changeset 31:f3f67aa3123b (2017-01-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c |
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modified:
macros.xml peptide_shaker.xml searchgui.xml test-data/peptide_shaker_certificate_result2.txt test-data/peptide_shaker_hierarchical_result2.tabular test-data/peptide_shaker_peptides_phoshorylation_result2.tabular test-data/peptide_shaker_peptides_result2.tabular test-data/peptide_shaker_proteins_phoshorylation_result2.tabular test-data/peptide_shaker_proteins_result2.tabular test-data/peptide_shaker_psm_phoshorylation_result2.tabular test-data/peptide_shaker_psm_result1.tabular test-data/peptide_shaker_psm_result2.tabular test-data/peptide_shaker_result1.zip test-data/searchgui_tinydb1.fasta test-data/tiny_searchgui_result1.zip test-data/tiny_searchgui_result_amandaonly.zip |
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removed:
test-data/peptide_shaker_result1.cps tool_dependencies.xml |
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| diff -r 78fad25eff17 -r ad60446b1e93 macros.xml --- a/macros.xml Fri Jun 10 09:58:03 2016 -0400 +++ b/macros.xml Fri Jan 13 14:15:42 2017 -0500 |
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| @@ -4,13 +4,18 @@ <exit_code range="1:" level="fatal" description="Job Failed" /> <regex match="java.*Exception" level="fatal" description="Java Exception"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> + <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> -frag_tol "${fragment_tol}" + ### -frag_ppm -prec_tol "${precursor_ion_tol}" -prec_ppm "${precursor_ion_tol_units}" + ### -digestion + ### multiple enzymes? -enzyme "${enzyme}" + ### -specificity #set $fixed_mods_str = $fixed_modifications or '' #set $variable_mods_str = $variable_modifications or '' #if $fixed_mods_str @@ -21,12 +26,13 @@ #end if -min_charge $min_charge -max_charge $max_charge + ### value per enzyme -mc $missed_cleavages -fi $forward_ion -ri $reverse_ion </token> - <token name="@SEARCHGUI_MAJOR_VERSION@">2</token> - <token name="@SEARCHGUI_VERSION@">2.9</token> + <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> + <token name="@SEARCHGUI_VERSION@">3.1.4</token> <xml name="general_options"> <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> |
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| diff -r 78fad25eff17 -r ad60446b1e93 peptide_shaker.xml --- a/peptide_shaker.xml Fri Jun 10 09:58:03 2016 -0400 +++ b/peptide_shaker.xml Fri Jan 13 14:15:42 2017 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">\n+<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">\n <description>\n Perform protein identification using various search engines based on results from SearchGUI\n </description>\n@@ -6,7 +6,7 @@\n <import>macros.xml</import>\n </macros>\n <requirements>\n- <requirement type="package" version="1.11">peptide_shaker</requirement>\n+ <requirement type="package" version="1.13.6">peptide-shaker</requirement>\n </requirements>\n <expand macro="stdio" />\n <command>\n@@ -15,36 +15,30 @@\n #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $temp_stderr = "peptideshaker_stderr"\n+ #set $bin_dir = "bin"\n \n \n mkdir output_reports;\n cwd=`pwd`;\n \n- cp -r "\\${PEPTIDESHAKER_JAR_PATH%/*}" bin;\n- tmp_peptideshaker_jar_path=`echo "\\$cwd/bin/\\${PEPTIDESHAKER_JAR_PATH\\#\\#/*/}"`;\n-\n ln -s \'$searchgui_input\' searchgui_input.zip &&\n+ jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&\n ######################\n ## PeptideShakerCLI ##\n ######################\n- (java -cp \\$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI\n+ (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI\n+ --exec_dir="\\$cwd/${bin_dir}"\n -temp_folder \\$cwd/PeptideShakerCLI\n -experiment \'$exp_str\'\n -sample \'$samp_str\'\n -replicate 1\n -identification_files \\$cwd/searchgui_input.zip\n+ -id_params \\$cwd/SEARCHGUI_IdentificationParameters.par\n -out \\$cwd/peptideshaker_output.cpsx\n -zip \\$cwd/peptideshaker_output.zip\n \n -threads "\\${GALAXY_SLOTS:-12}"\n \n- ##Optional gene annotation parameter\n- #if $species_type.species_type_selector != \'no_species_type\':\n- -species_type "${species_type.species_type_selector}"\n- -species "${species_type.species}"\n- -species_update 1\n- #end if\n-\n ##Optional processing parameters:\n #if $processing_options.processing_options_selector == "yes"\n -protein_fdr "${processing_options.protein_fdr}"\n@@ -85,16 +79,33 @@\n \n #if \'mzidentML\' in str($outputs).split(\',\'):\n echo "Generating mzIdentML";\n- (java -cp \\$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI\n+ (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI\n+ --exec_dir="\\$cwd/${bin_dir}"\n -in \\$cwd/peptideshaker_output.zip\n -output_file output.mzid\n- -contact_first_name "Proteomics"\n- -contact_last_name "Galaxy"\n- -contact_email "galaxyp@umn.edu"\n- -contact_address "galaxyp@umn.edu"\n- -organization_name "University of Minnesota"\n- -organization_email "galaxyp@umn.edu"\n- -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"\n+ #if $contact_options.contact_options_selector == "yes":\n+ -contact_first_name "$contact_options.contact_first_name"\n+ -contact_last_name "$contact_options.contact_last_name"\n+ -contact_email "$contact_options.contact_email"\n+ -contact_address "$contact_options.contact_address"\n+ #if str($contact_options.contact_url).strip() != \'\':\n+ -contact_url = "$contact_options.contact_url"\n+ #end if\n+ -organization_name "$contact_options.organization_name"\n+ -organization_email "$contact_options.organization_email"\n+ -organization_address "$contact_options.o'..b'tein Phosphorylation Report</option>\n <option value="0">Certificate of Analysis</option>\n <option value="1">Hierarchical Report</option>\n <option value="cps">CPS file</option>\n@@ -541,6 +315,9 @@\n <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">\n <filter>\'3\' in outputs</filter>\n </data>\n+ <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">\n+ <filter>\'8\' in outputs</filter>\n+ </data>\n <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">\n <filter>\'4\' in outputs</filter>\n </data>\n@@ -557,17 +334,14 @@\n <tests>\n <test>\n <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>\n- <param name="species_type_selector" value="no_species_type"/>\n <param name="processing_options_selector" value="no"/>\n <param name="filtering_options_selector" value="no"/>\n- <param name="outputs" value="zip,cps,3"/>\n+ <param name="outputs" value="zip,3"/>\n <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" />\n- <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" />\n <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />\n </test>\n <test>\n <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>\n- <param name="species_type_selector" value="no_species_type"/>\n <param name="processing_options_selector" value="no"/>\n <param name="filtering_options_selector" value="yes"/>\n <param name="min_peptide_length" value="1"/>\n@@ -581,25 +355,14 @@\n <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />\n <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />\n </test>\n- <test>\n- <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>\n- <param name="species_type_selector" value="Vertebrates"/>\n- <param name="species" value="Human (Homo sapiens)"/>\n- <param name="processing_options_selector" value="no"/>\n- <param name="filtering_options_selector" value="yes"/>\n- <param name="min_peptide_length" value="1"/>\n- <param name="outputs" value="5"/>\n- <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" />\n- </test>\n </tests>\n <help>\n **What it does**\n \n Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.\n \n-https://code.google.com/p/peptide-shaker/\n-\n-https://code.google.com/p/searchgui/\n+http://compomics.github.io/projects/peptide-shaker.html\n+http://compomics.github.io/projects/searchgui.html\n \n ----\n \n@@ -746,9 +509,9 @@\n \n **Citation**\n \n-To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com \n+To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io\n \n-If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker\n+If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.\n </help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 78fad25eff17 -r ad60446b1e93 searchgui.xml --- a/searchgui.xml Fri Jun 10 09:58:03 2016 -0400 +++ b/searchgui.xml Fri Jan 13 14:15:42 2017 -0500 |
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| b'@@ -7,7 +7,6 @@\n </macros>\n <requirements>\n <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>\n- <environment_variable name="LC_ALL" action="set_to">C</environment_variable> \n </requirements>\n <expand macro="stdio" />\n <command>\n@@ -16,21 +15,25 @@\n #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $temp_stderr = "searchgui_stderr"\n+ #set $bin_dir = "bin"\n \n mkdir output;\n mkdir output_reports;\n cwd=`pwd`;\n export HOME=\\$cwd;\n \n+ ## echo the search engines to run\n+ echo "$engines";\n+ echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";\n+\n ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present\n echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;\n \n- cp -r "\\${SEARCHGUI_JAR_PATH%/*}" bin;\n- tmp_searchgui_jar_path=`echo "\\$cwd/bin/\\${SEARCHGUI_JAR_PATH\\#\\#/*/}"`;\n-\n #for $mgf in $peak_lists:\n #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"\n ln -s -f \'${mgf}\' \'${input_name}\';\n+ #set $encoded_id = $__app__.security.encode_id($mgf.id)\n+ echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";\n #end for\n ##ln -s "${input_database}" input_database.fasta;\n cp "${input_database}" input_database.fasta;\n@@ -40,7 +43,7 @@\n ###########################################\n #if $create_decoy:\n echo "Creating decoy database.";\n- java -cp \\$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&\n+ searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\\$cwd/${bin_dir}" -in input_database.fasta -decoy &&\n rm input_database.fasta &&\n cp input_database_concatenated_target_decoy.fasta input_database.fasta &&\n ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;\n@@ -49,14 +52,17 @@\n #####################################################\n ## generate IdentificationParameters for SearchGUI ##\n #####################################################\n-\n- (java -cp \\$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI\n+ (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI\n+ --exec_dir="\\$cwd/${bin_dir}"\n -out SEARCHGUI_IdentificationParameters.par\n \n @GENERAL_PARAMETERS@\n \n -db input_database.fasta\n- $use_gene_mapping\n+ #if $use_gene_mapping:\n+ $use_gene_mapping\n+ $update_gene_mapping\n+ #end if\n \n #if $xtandem.xtandem_advanced == "yes"\n \n@@ -196,6 +202,7 @@\n -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}\n -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}\n -andromeda_max_psms ${andromeda.andromeda_max_psms}\n+ -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode}\n #end if\n *#\n \n@@ -245,15 +252,16 @@\n #if $comet.comet_spectrum.comet_spectrum_selector == "yes"\n -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}\n -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}\n- -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec}\n+\n+ -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec}\n \n \n- #if $comet.comet_spectrum.comet_remove_prec == "1"\n- -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}\n+ #if $comet.comet'..b'M spectrum, default is false."/>\n+ <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>\n+ <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">\n+ <option value="0" selected="true">no deisotoping</option>\n+ <option value="1">precursor only</option>\n+ <option value="2">precursor and candidate</option>\n+ </param>\n+ <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is \'0.25\'."/>\n+ <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is \'0.5\'."/>\n+ <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is \'3\'."/>\n+ <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is \'2\'."/>\n+ <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is \'20\'."/>\n+ <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is \'1.0\'."/>\n+ <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is \'1.0\'."/>\n+ <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is \'1.0\'."/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="novor">\n+ <param name="novor_advanced" type="select" label="Novor Options">\n+ <option value="yes">Advanced</option>\n+ <option value="no" selected="True">Default</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <param name="novor_fragmentation" type="select" label="Novor fragmentation method">\n+ <option value="HCD" selected="True">HCD</option>\n+ <option value="CID">CID</option>\n+ </param>\n+ <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">\n+ <option value="FT" selected="True">FT</option>\n+ <option value="Trap" >Trap</option>\n+ <option value="TOF" >TOF</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n </inputs>\n <outputs>\n <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />\n@@ -983,9 +1100,8 @@\n <param name="xtandem.xtandem_advanced" value="yes"/>\n <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>\n \n- <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> \n+ <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> \n </test>\n-\n <!-- Test that search works with MSAmanda -->\n <test>\n <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>\n@@ -997,10 +1113,8 @@\n <param name="max_charge" value="3"/>\n <param name="engines" value="MS_Amanda"/>\n \n- <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> \n+ <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> \n </test>\n-\n-\n </tests>\n <help>\n **What it does**\n' |
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| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_certificate_result2.txt --- a/test-data/peptide_shaker_certificate_result2.txt Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_certificate_result2.txt Fri Jan 13 14:15:42 2017 -0500 |
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| @@ -1,67 +1,68 @@ -Project Details1: PeptideShaker Version: 0.39.1 -2: Date: Thu Jun 04 20:07:16 CEST 2015 -3: Experiment: Galaxy_Experiment_2015060420071433441234 -4: Sample: Sample_2015060420071433441234 +Project Details1: PeptideShaker Version: 1.13.6 +2: Date: Fri Jan 13 11:06:50 CST 2017 +3: Experiment: Galaxy_Experiment_2017011311051484327131 +4: Sample: Sample_2017011311051484327131 5: Replicate Number: 1 -6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet +6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+, Comet and MyriMatch Database Search Parameters -1: Precursor Accuracy Unit: ppm +1: Precursor Tolerance Unit: ppm 2: Precursor Ion m/z Tolerance: 100.0 -3: Fragment Ion m/z Tolerance: 0.5 -4: Enzyme: Trypsin -5: Number of Missed Cleavages: Not implemented -6: Database: input_database.fasta -7: Forward Ion: b -8: Rewind Ion: y -9: Fixed Modifications: carbamidomethyl c -10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q -11: Refinement Variable Modifications: -12: Refinement Fixed Modifications: +3: Fragment Ion Tolerance Unit: Da +4: Fragment Ion m/z Tolerance: 0.5 +5: Enzyme: Trypsin +6: Maximum Missed Cleavages: 2 +7: Database: input_database.fasta +8: Forward Ion: b +9: Rewind Ion: y +10: Fixed Modifications: Carbamidomethylation of C +11: Variable Modifications: Oxidation of M, Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C +12: Refinement Variable Modifications: +13: Refinement Fixed Modifications: Input Filters 1: Minimal Peptide Length: 1 2: Maximal Peptide Length: 30 3: Precursor m/z Tolerance: 10.0 4: Precursor m/z Tolerance Unit: Yes -5: Unrecognized Modifications Discarded: No +5: Unrecognized Modifications Discarded: Yes Validation Summary -1: #Validated Proteins: 0.0 -2: Protein Total: 0.0 -3Protein FDR Limit: 1.0 % -4: Protein FNR Limit: 0.0 % -5: Protein Confidence Limit: -1.0 % -6: Protein PEP Limit: 101.0 % -7: Protein Confidence Accuracy: 0.0 % -8: #Validated Peptides: 0.0 -9: Peptide Total: 0.0 -10: Peptide FDR Limit: 1.0 % -11: Peptide FNR Limit: 0.0 % -12: Peptide Confidence Limit: -1.0 % -13: Peptide PEP Limit: 101.0 % -14: Peptide Confidence Accuracy: 0.0 % -15: #Validated PSM: 0.0 -16: PSM Total: 0.0 -17: PSM FDR Limit: 1.0 % -18: PSM FNR Limit: 0.0 % -19: PSM Confidence Limit: -1.0 % -20: PSM PEP Limit: 101.0 % -21: PSM Confidence Accuracy: 0.0 % -Postranslational Modification Scoring Settings +1: Proteins: #Validated: 2.0 +2: Proteins: Total Possible TP: 2.0 +3: Proteins: FDR Limit [%]: 0.0 +4: Proteins: FNR Limit [%]: 0.0 +5: Proteins: Confidence Limit [%]: 100.0 +6: Proteins: PEP Limit [%]: 0.0 +7: Proteins: Confidence Accuracy [%]: 0.0 +8: Peptides: #Validated: 16.0 +9: Peptides: Total Possible TP: 16.0 +10: Peptides: FDR Limit [%]: 0.0 +11: Peptides: FNR Limit [%]: 0.0 +12: Peptides: Confidence Limit [%]: 100.0 +13: Peptides: PEP Limit [%]: 0.0 +14: Peptides: Confidence Accuracy [%]: 0.0 +15: PSMs: #Validated PSM: 42.0 +16: PSMs: Total Possible TP: 42.0 +17: PSMs: FDR Limit [%]: 0.0 +18: PSMs: FNR Limit [%]: 0.0 +19: PSMs: Confidence Limit [%]: 100.0 +20: PSMs: PEP Limit [%]: 0.0 +21: PSMs: Confidence Accuracy [%]: 0.0 +PTM Scoring Settings -1: A-score: No +1: Probabilistic Score: PhosphoRS 2: Accounting for Neutral Losses: No -3: False Location Rate: 1.0 +3: Threshold: 95.0 Spectrum Counting Parameters 1: Method: NSAF -2: Validated Matches Only: Yes +2: Validated Matches Only: No Annotation Settings 1: Intensity Limit: 0.75 2: Automatic Annotation: Yes -3: Selected Ions: b, y -4: Neutral Losses: H2O, NH3 +3: Selected Ions: y, b +4: Neutral Losses: H2O, NH3, CH4OS 5: Neutral Losses Sequence Dependence: Yes 6: Fragment Ion m/z Tolerance: 0.5 |
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| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_hierarchical_result2.tabular --- a/test-data/peptide_shaker_hierarchical_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_hierarchical_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| b'@@ -1,79 +1,79 @@\n-\tMain Accession\tDescription\tMW [kDa]\tPossible Coverage [%]\tCoverage [%]\tSpectrum Counting NSAF \tConfidently Localized Modification Sites\t# Confidently Localized Modification Sites\tAmbiguously Localized Modification Sites\t#Ambiguously Localized Modification Sites\tPI\tSecondary Accessions\tProtein Group\t#Validated Peptides\t#Peptides\t#Unique\t#Validated PSMs\t#PSMs\tConfidence\tDecoy\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\t\t69.88215372568374\t92.52\t37.58\t0.01785479771710408\t\t\t\t\tRelated Proteins\tcds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\t15\t15\t15\t40\t40\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence\tDecoy\tValidation\n-1.1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tAK; AK\tIS; IS\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tprobabilistic PTM score\tD-score\tConfidence\tValidation\n-1.1.1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 204, MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\t0\t\t\t\t100.0\tDoubtful\n-1.1.2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 207, MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362346836998\t0\t-9.522288910374096\t0\t\t\t\t100.0\tDoubtful\n-1.1.3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\t0\t\t\t\t100.0\tDoubtful\n-1.1.4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 207, +MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362346836998\t0\t-9.522288910374096\t0\t\t\t\t100.0\tDoubtful\n-1.2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\t'..b'\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t0\t\t\t\t100.0\tDoubtful\n+1.14\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tSK; SK; SK\tSK; SK; SK\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+\tProtein(s)\tSequence\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n+1.14.1\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t0\t\t\t\t100.0\tDoubtful\n+1.14.2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t0\t\t\t\t100.0\tDoubtful\n+1.15\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tLISATSISPEHK\tDR; DR; DR\tID; ID; ID\t\t\t\t4\t4\t100.0\t0\tDoubtful\n+\tProtein(s)\tSequence\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n+1.15.1\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.4810042052113237\t0\t\t\t\t100.0\tDoubtful\n+1.15.2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, +MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t0\t\t\t\t100.0\tDoubtful\n+1.15.3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.4810042052113237\t0\t\t\t\t100.0\tDoubtful\n+1.15.4\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t0\t\t\t\t100.0\tDoubtful\n+2\tcds.comp52727_c0_seq1\tm.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91\t69.96963713242043\t100.0\t3.25\t0.0032520325203252032\t\t\t\t\tRelated Proteins\tcds.comp52727_c0_seq2\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\t1\t1\t1\t2\t2\t100.0\t0\tDoubtful\n+\tProtein(s)\tSequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence [%]\tDecoy\tValidation\n+2.1\tcds.comp52727_c0_seq1; cds.comp52727_c0_seq2\tEIRDEYDNQLNLLSADLESK\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+\tProtein(s)\tSequence\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n+2.1.1\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444984557097\t0\t6.206637734347747\t0\t\t\t\t100.0\tDoubtful\n+2.1.2\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444984557097\t0\t6.206637734347747\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_peptides_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| b'@@ -1,17 +1,17 @@\n-\tProtein(s)\tSequence\tModified Sequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\tConfident Phosphosites\t#Confident Phosphosites\tAmbiguous Phosphosites\t#Ambiguous Phosphosites\t#Validated PSMs\t#PSMs\tConfidence\tDecoy\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\tAK; AK\tIS; IS\t\t\t\t\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNH2-ISTGYITENIGGFR-COOH\tNR; NR\tSE; SE\t\t\t\t\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-3\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\tMR; MR\tYQ; YQ\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\tAR; AR\tLI; LI\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\tRR; RR\tAS; AS\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\tDR; DR; DR\tID; ID; ID\t\t\t\t\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-8\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-9\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\tSK; SK; SK\tSK; SK; SK\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-10\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kD'..b'70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-16\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+\tProtein(s)\tProtein Group(s)\t#Validated Protein Group(s)\tUnique Database\tSequence\tModified Sequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\tConfident Phosphosites\t#Confident Phosphosites\tAmbiguous Phosphosites\t#Ambiguous Phosphosites\t#Validated PSMs\t#PSMs\tConfidence [%]\tValidation\n+1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\tSK; SK; SK\tSK; SK; SK\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+2\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tYESQLSQIR\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+3\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\tRR; RR\tAS; AS\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+4\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\tRR; RR\tNL; NL\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+5\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+6\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tISTGYITENIGGFR\tNH2-ISTGYITENIGGFR-COOH\tNR; NR\tSE; SE\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n+7\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tASLGMAAGVAGGIATK\tNH2-ASLGMAAGVAGGIATK-COOH\tGR; GR\tDM; DM\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+8\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\tDR; DR; DR\tID; ID; ID\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n+9\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\tNK; NK\tLS; LS\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n+10\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\tAK; AK\tIS; IS\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n+11\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+12\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\tAK; AK; AK\tNS; NS; NS\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+13\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+14\tcds.comp52727_c0_seq1; cds.comp52727_c0_seq2\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2 (Doubtful)\t1\t1\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\tMR; MR\tYQ; YQ\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n+15\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n+16\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\tAR; AR\tLI; LI\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n' |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_peptides_result2.tabular --- a/test-data/peptide_shaker_peptides_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_peptides_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| b'@@ -1,17 +1,17 @@\n-\tProtein(s)\tSequence\tModified Sequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence\tDecoy\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\tAK; AK\tIS; IS\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNH2-ISTGYITENIGGFR-COOH\tNR; NR\tSE; SE\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-3\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\tAR; AR\tLI; LI\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\tRR; RR\tAS; AS\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\tDR; DR; DR\tID; ID; ID\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-8\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-9\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\tSK; SK; SK\tSK; SK; SK\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-10\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK'..b'ull=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-16\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+\tProtein(s)\tProtein Group(s)\t#Validated Protein Group(s)\tUnique Database\tSequence\tModified Sequence\tPosition\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence [%]\tValidation\n+1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t511; 504; 29\tSK; SK; SK\tSK; SK; SK\t\t\t\t2\t2\t100.0\tDoubtful\n+2\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tYESQLSQIR\tNH2-YESQLSQIR-COOH\t323; 323\tAR; AR\tQS; QS\t\t\t\t2\t2\t100.0\tDoubtful\n+3\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\t37; 37\tRR; RR\tAS; AS\t\t\t\t2\t2\t100.0\tDoubtful\n+4\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t128; 128\tRR; RR\tNL; NL\t\t\t\t2\t2\t100.0\tDoubtful\n+5\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\t161; 161\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\tDoubtful\n+6\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tISTGYITENIGGFR\tNH2-ISTGYITENIGGFR-COOH\t442; 442\tNR; NR\tSE; SE\t\t\t\t4\t4\t100.0\tDoubtful\n+7\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tASLGMAAGVAGGIATK\tNH2-ASLGMAAGVAGGIATK-COOH\t63; 63\tGR; GR\tDM; DM\t\t\t\t2\t2\t100.0\tDoubtful\n+8\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t549; 542; 67\tDR; DR; DR\tID; ID; ID\t\t\t\t4\t4\t100.0\tDoubtful\n+9\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\t403; 403\tNK; NK\tLS; LS\t\t\t\t4\t4\t100.0\tDoubtful\n+10\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t147; 147\tAK; AK\tIS; IS\t\t\t\t4\t4\t100.0\tDoubtful\n+11\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\t110; 110\tVR; VR\tLK; LK\t\t\t\t2\t2\t100.0\tDoubtful\n+12\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\t590; 583; 108\tAK; AK; AK\tNS; NS; NS\t\t\t\t2\t2\t100.0\tDoubtful\n+13\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\t373; 373\tMK; MK\tSN; SN\t\t\t\t2\t2\t100.0\tDoubtful\n+14\tcds.comp52727_c0_seq1; cds.comp52727_c0_seq2\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2 (Doubtful)\t1\t1\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t298; 298\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\tDoubtful\n+15\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\t254; 254\tQK; QK\tSV; SV\t\t\t\t4\t4\t100.0\tDoubtful\n+16\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful)\t1\t1\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\t179; 179\tAR; AR\tLI; LI\t\t\t\t2\t2\t100.0\tDoubtful\n' |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_proteins_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| @@ -1,3 +1,3 @@ - Main Accession Description Gene Name Chromosome MW [kDa] Possible Coverage [%] Coverage [%] Spectrum Counting NSAF Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation -1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 92.52 37.58 0.01785479771710408 0 0 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 40 40 100.0 0 Doubtful -2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 100.0 3.25 0.0032520325203252032 0 0 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful + Main Accession Description Gene Name Chromosome MW [kDa] Possible Coverage [%] Coverage [%] Spectrum Counting NSAF Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites Protein Inference Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated Unique #Unique to Group #Validated Unique to Group #Validated PSMs #PSMs Confidence [%] Validation +1 cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215380565927 92.52 37.58 0.017651472642866785 0 0 Related Proteins cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 15 15 15 15 15 15 40 40 100.0 Doubtful +2 cds.comp52727_c0_seq1 m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.96963713242043 100.0 3.25 0.0032520325203252032 0 0 Related Proteins cds.comp52727_c0_seq2 cds.comp52727_c0_seq1, cds.comp52727_c0_seq2 1 1 1 1 1 1 2 2 100.0 Doubtful |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_proteins_result2.tabular --- a/test-data/peptide_shaker_proteins_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_proteins_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| @@ -1,3 +1,3 @@ - Main Accession Description Gene Name Chromosome MW [kDa] Possible Coverage [%] Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated PSMs #PSMs Confidence Decoy Validation -1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215372568374 92.52 37.58 0.01785479771710408 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 40 40 100.0 0 Doubtful -2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.9696370486838 100.0 3.25 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful + Main Accession Description Gene Name Chromosome MW [kDa] Possible Coverage [%] Coverage [%] Spectrum Counting Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites Protein Inference Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #Validated Unique #Unique to Group #Validated Unique to Group #Validated PSMs #PSMs Confidence [%] Validation +1 cds.comp41779_c0_seq1 m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 69.88215380565927 92.52 37.58 24162.449974467898 Related Proteins cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 15 15 15 15 15 15 40 40 100.0 Doubtful +2 cds.comp52727_c0_seq1 m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.96963713242043 100.0 3.25 4451.587393160344 Related Proteins cds.comp52727_c0_seq2 cds.comp52727_c0_seq1, cds.comp52727_c0_seq2 1 1 1 1 1 1 2 2 100.0 Doubtful |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_psm_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| b'@@ -1,43 +1,43 @@\n-\tProtein(s)\tSequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tprobabilistic PTM score\tD-score\tConfident Phosphosites\t#Confident Phosphosites\tAmbiguous Phosphosites\t#Ambiguous Phosphosites\tConfidence\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 204, MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7728996836997\t0\t2.458444778796749\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-3\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7728996836997\t0\t3.1184077735785474\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326546837003\t0\t-1.7717994436305495\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 220, MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263816837\t0\t2.9391347559636922\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 75, MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928656837001\t0\t1.4811651380377848\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-8\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.'..b'2\t0\t1.6439836590138295\t\t\t\t\t\t\t\t100.0\tDoubtful\n+25\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t\t\t\t\t100.0\tDoubtful\n+26\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.4810042052113237\t\t\t\t\t\t\t\t100.0\tDoubtful\n+27\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tYESQLSQIR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127984108653\t\t\t\t\t\t\t\t100.0\tDoubtful\n+28\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSLQAENEQLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.0634108237361883\t\t\t\t\t\t\t\t100.0\tDoubtful\n+29\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tYESQLSQIR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127984108653\t\t\t\t\t\t\t\t100.0\tDoubtful\n+30\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 871, +MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354589782603\t0\t1.7035983403308754\t\t\t\t\t\t\t\t100.0\tDoubtful\n+31\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tKGDIIATVDEWGPVNR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t\t\t\t\t\t\t\t100.0\tDoubtful\n+32\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.1135461012602375\t\t\t\t\t\t\t\t100.0\tDoubtful\n+33\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t\t\t\t\t100.0\tDoubtful\n+34\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t\t\t\t\t100.0\tDoubtful\n+35\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t\t\t\t\t100.0\tDoubtful\n+36\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t\t\t\t\t\t\t\t100.0\tDoubtful\n+37\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t\t\t\t\t100.0\tDoubtful\n+38\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, +MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t\t\t\t\t100.0\tDoubtful\n+39\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t\t\t\t\t\t\t\t100.0\tDoubtful\n+40\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, +MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t\t\t\t\t\t\t\t100.0\tDoubtful\n+41\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSLQAENEQLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.0634108237361883\t\t\t\t\t\t\t\t100.0\tDoubtful\n+42\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, +MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_psm_result1.tabular --- a/test-data/peptide_shaker_psm_result1.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_psm_result1.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| b'@@ -1,43 +1,43 @@\n-\tProtein(s)\tSequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tprobabilistic PTM score\tD-score\tConfidence\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 204, MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\t0\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7728996836997\t0\t2.458444778796749\t0\t\t\t\t100.0\tDoubtful\n-3\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7728996836997\t0\t3.1184077735785474\t0\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326546837003\t0\t-1.7717994436305495\t0\t\t\t\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 220, MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263816837\t0\t2.9391347559636922\t0\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 75, MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928656837001\t0\t1.4811651380377848\t0\t\t\t\t100.0\tDoubtful\n-8\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\t\t\t\t100.0\tDoubtful\n-9\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament p'..b'2\t0\t6.998127984108653\t\t\t\t100.0\tDoubtful\n+28\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n+29\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127984108653\t\t\t\t100.0\tDoubtful\n+30\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\tQK; QK\tSV; SV\t254; 254\tNH2-VGNLEEELEFLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 871, +MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354589782603\t0\t1.7035983403308754\t\t\t\t100.0\tDoubtful\n+31\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tKGDIIATVDEWGPVNR\tAK; AK; AK\tNS; NS; NS\t590; 583; 108\tNH2-KGDIIATVDEWGPVNR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t\t\t\t100.0\tDoubtful\n+32\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.1135461012602375\t\t\t\t100.0\tDoubtful\n+33\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tSK; SK; SK\tSK; SK; SK\t511; 504; 29\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t100.0\tDoubtful\n+34\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n+35\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n+36\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t\t\t\t100.0\tDoubtful\n+37\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n+38\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\tGR; GR\tDM; DM\t63; 63\tNH2-ASLGMAAGVAGGIATK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, +MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t100.0\tDoubtful\n+39\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t\t\t\t100.0\tDoubtful\n+40\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tDR; DR; DR\tID; ID; ID\t549; 542; 67\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, +MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t\t\t\t100.0\tDoubtful\n+41\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n+42\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, +MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_psm_result2.tabular --- a/test-data/peptide_shaker_psm_result2.tabular Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/peptide_shaker_psm_result2.tabular Fri Jan 13 14:15:42 2017 -0500 |
| [ |
| b'@@ -1,43 +1,43 @@\n-\tProtein(s)\tSequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tprobabilistic PTM score\tD-score\tConfidence\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 204, MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\t0\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7728996836997\t0\t2.458444778796749\t0\t\t\t\t100.0\tDoubtful\n-3\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7728996836997\t0\t3.1184077735785474\t0\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326546837003\t0\t-1.7717994436305495\t0\t\t\t\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 220, MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263816837\t0\t2.9391347559636922\t0\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 75, MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928656837001\t0\t1.4811651380377848\t0\t\t\t\t100.0\tDoubtful\n-8\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\t\t\t\t100.0\tDoubtful\n-9\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament p'..b'2\t0\t6.998127984108653\t\t\t\t100.0\tDoubtful\n+28\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n+29\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127984108653\t\t\t\t100.0\tDoubtful\n+30\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\tQK; QK\tSV; SV\t254; 254\tNH2-VGNLEEELEFLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 871, +MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354589782603\t0\t1.7035983403308754\t\t\t\t100.0\tDoubtful\n+31\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tKGDIIATVDEWGPVNR\tAK; AK; AK\tNS; NS; NS\t590; 583; 108\tNH2-KGDIIATVDEWGPVNR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t\t\t\t100.0\tDoubtful\n+32\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.1135461012602375\t\t\t\t100.0\tDoubtful\n+33\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tSK; SK; SK\tSK; SK; SK\t511; 504; 29\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t100.0\tDoubtful\n+34\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n+35\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n+36\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t\t\t\t100.0\tDoubtful\n+37\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n+38\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\tGR; GR\tDM; DM\t63; 63\tNH2-ASLGMAAGVAGGIATK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, +MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t100.0\tDoubtful\n+39\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t\t\t\t100.0\tDoubtful\n+40\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tDR; DR; DR\tID; ID; ID\t549; 542; 67\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, +MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t\t\t\t100.0\tDoubtful\n+41\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n+42\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, +MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n' |
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| diff -r 78fad25eff17 -r ad60446b1e93 test-data/peptide_shaker_result1.cps |
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| diff -r 78fad25eff17 -r ad60446b1e93 test-data/searchgui_tinydb1.fasta --- a/test-data/searchgui_tinydb1.fasta Fri Jun 10 09:58:03 2016 -0400 +++ b/test-data/searchgui_tinydb1.fasta Fri Jan 13 14:15:42 2017 -0500 |
| b |
| @@ -1,24 +1,24 @@ ->cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 +>generic|cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV ->cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 +>generic|cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ ->cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 +>generic|cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR ->cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 +>generic|cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 +>generic|cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 +>generic|cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 +>generic|cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL ->cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 +>generic|cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 +>generic|cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 +>generic|cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ ->cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 +>generic|cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN ->cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 +>generic|cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP |
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| diff -r 78fad25eff17 -r ad60446b1e93 tool_dependencies.xml --- a/tool_dependencies.xml Fri Jun 10 09:58:03 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="searchgui" version="2.9"> - <repository changeset_revision="a04e562f2ff0" name="package_searchgui_2_9" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="peptide_shaker" version="1.11"> - <repository changeset_revision="bd41b685f845" name="package_peptideshaker_1_11" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |