| Previous changeset 19:7e61179c5952 (2014-06-25) Next changeset 21:dfaea053e32f (2015-06-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b |
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modified:
peptide_shaker.xml repository_dependencies.xml tool_dependencies.xml |
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added:
README.rst admin_scripts/build_mods_loc.py admin_scripts/build_species.py admin_scripts/searchGUI_mods.xml admin_scripts/searchGUI_usermods.xml admin_scripts/species macros.xml searchgui.xml test-data/peptide_shaker_certificate_result2.tabular 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_peptides_result3.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.cps test-data/peptide_shaker_result1.zip test-data/searchgui_tinydb1.fasta test-data/searchgui_tinyspectra1.mgf test-data/tiny_searchgui_result1.zip |
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removed:
README.md test-data/._tinyoutput.cps test-data/tinydb.fasta test-data/tinyoutput.cps test-data/tinyspectra.mgf |
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| diff -r 7e61179c5952 -r 2cafc729b2ae README.md --- a/README.md Wed Jun 25 11:50:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,74 +0,0 @@ -GalaxyP - PeptideShaker -======================= - -* Home: <https://bitbucket.org/galaxyp/peptideshaker> -* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> -* Tool ID: `peptideshaker` -* Tool Type: `default` - - -Description ------------ - -Perform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. - -Tool wrapper for SearchGUI and PeptideShaker. This tool takes any number of mgf files and performs X! Tandem and OMSSA searches on these via SearchGUI and merges the results using PeptideShaker. - -Configuration -------------- - -This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell; - -export _JAVA_OPTIONS='-Xmx1500M' - -It is also possible to set this on a per tool basis using advanced features of the galaxy job config system - -Note: - -- SearchGUI requires a version greater than 1.12.2 which contained several bugs preventing this from working on the command-line and via Linux. - -- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. - -See: - -* <https://code.google.com/p/peptide-shaker/> -* <https://code.google.com/p/searchgui/> - - -GalaxyP Community ------------------ - -Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: - -<https://bitbucket.org/galaxyp/galaxyp> - - -License -------- - -Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. - -To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. - -You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. - -You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. - - -Contributing ------------- - -Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. - - -Authors -------- - -Authors and contributors: - -* Bjoern Gruening <bjoern.gruening@gmail.com> -* Ira Cooke -* Cody Wang -* Fred Sadler -* John Chilton <jmchilton@gmail.com> -* Minnesota Supercomputing Institute, Univeristy of Minnesota |
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| diff -r 7e61179c5952 -r 2cafc729b2ae README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun May 31 09:05:57 2015 -0400 |
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| @@ -0,0 +1,78 @@ +GalaxyP - PeptideShaker +======================= + +- Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +- Tool ID: `peptideshaker`, `search_gui` + + +Description +----------- + +Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker. + +Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference. + + +Configuration +------------- + +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: + + export _JAVA_OPTIONS='-Xmx1500M' + +On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example: + + export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M' + +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. + +Note: + +- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. + +See: + +* <https://code.google.com/p/peptide-shaker/> +* <https://code.google.com/p/searchgui/> + + +GalaxyP Community +----------------- + +Current governing community policies for GalaxyP_ and other information can be found at: + +<https://github.com/galaxyproteomics> + +.. _GalaxyP: https://github.com/galaxyproteomics/ + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* Bjoern Gruening <bjoern.gruening@gmail.com> +* Ira Cooke +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota |
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| diff -r 7e61179c5952 -r 2cafc729b2ae admin_scripts/build_mods_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/build_mods_loc.py Sun May 31 09:05:57 2015 -0400 |
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| @@ -0,0 +1,12 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +with open("searchgui_mods.loc.sample", "w") as output: + for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]: + tree = ET.parse(mods_path) + modifications_el = tree.getroot() + for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"): + name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name") + output.write("%s\n" % name_el.text.lower()) |
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| diff -r 7e61179c5952 -r 2cafc729b2ae admin_scripts/build_species.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/build_species.py Sun May 31 09:05:57 2015 -0400 |
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| @@ -0,0 +1,10 @@ +#!/usr/bin/env python + +import sys + +for line in open( sys.argv[1] ): + line = line.strip() + if line and not line.startswith('>'): + name, id = line.split('\t') + line = '<option value="%s">%s</option>' % (name, name) + print line |
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| diff -r 7e61179c5952 -r 2cafc729b2ae admin_scripts/searchGUI_mods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/searchGUI_mods.xml Sun May 31 09:05:57 2015 -0400 |
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| b'@@ -0,0 +1,3021 @@\n+<?xml version="1.0"?>\n+<MSModSpecSet\n+ xmlns="http://www.ncbi.nlm.nih.gov"\n+ xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"\n+ xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"\n+ >\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="methylk">0</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>methylation of K</MSModSpec_name>\n+ <MSModSpec_monomass>14.015650</MSModSpec_monomass>\n+ <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>K</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>34</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="oxym">1</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>oxidation of M</MSModSpec_name>\n+ <MSModSpec_monomass>15.994915</MSModSpec_monomass>\n+ <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>M</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>35</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="carboxymethylc">2</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>carboxymethyl C</MSModSpec_name>\n+ <MSModSpec_monomass>58.005479</MSModSpec_monomass>\n+ <MSModSpec_averagemass>58.0361</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>6</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Carboxymethyl</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="carbamidomethylc">3</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>carbamidomethyl C</MSModSpec_name>\n+ <MSModSpec_monomass>57.021464</MSModSpec_monomass>\n+ <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>4</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="deamidationkq">4</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>deamidation of N and Q</MSModSpec_name>\n+ <MSModSpec_monomass>0.984016</MSModSpec_monomass>\n+ <MSModSpec_averagemass>0.9848</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>N</MSModSpec_residues_E>\n+ <MSModSpec_residues_E>Q</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>7</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Deamidated</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="propionamidec">5</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSMo'..b'dSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>K</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>730</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod202">202</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(7)15N(1) on Y</MSModSpec_name>\n+ <MSModSpec_monomass>304.205360</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3074</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>Y</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>730</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod203">203</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modnp">5</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on nterm</MSModSpec_name>\n+ <MSModSpec_monomass>304.199040</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_unimod>731</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod204">204</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on K</MSModSpec_name>\n+ <MSModSpec_monomass>304.199040</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>K</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>731</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod205">205</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on Y</MSModSpec_name>\n+ <MSModSpec_monomass>304.199040</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>Y</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>731</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod206">206</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>selenocysteine</MSModSpec_name>\n+ <MSModSpec_monomass>47.944449</MSModSpec_monomass>\n+ <MSModSpec_averagemass>46.8950</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>162</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod207">207</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>carboxymethylated selenocysteine</MSModSpec_name>\n+ <MSModSpec_monomass>105.949928</MSModSpec_monomass>\n+ <MSModSpec_averagemass>104.9311</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ </MSModSpec>\n+</MSModSpecSet>\n' |
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| diff -r 7e61179c5952 -r 2cafc729b2ae admin_scripts/searchGUI_usermods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/searchGUI_usermods.xml Sun May 31 09:05:57 2015 -0400 |
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| b'@@ -0,0 +1,455 @@\n+<?xml version="1.0"?>\n+<MSModSpecSet\n+xmlns="http://www.ncbi.nlm.nih.gov"\n+xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"\n+xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"\n+>\n+\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod1">119</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modnp">5</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>dimethyl 2d n-terminus</MSModSpec_name>\n+\t\t<MSModSpec_monomass>32.0564</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod2">120</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>dimethyl 2d k</MSModSpec_name>\n+\t\t<MSModSpec_monomass>32.0564</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>K</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod3">121</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>gtp desthiobiotinc12</MSModSpec_name>\n+\t\t<MSModSpec_monomass>196.121178</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>K</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod4">122</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>gtp desthiobiotinc13</MSModSpec_name>\n+\t\t<MSModSpec_monomass>202.141307</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>K</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod5">123</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 5</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod6">124</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 6</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod7">125</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 7</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod8">126</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 8</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</M'..b'es_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod23">154</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 23</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod24">155</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 24</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod25">156</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 25</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod26">157</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 26</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod27">158</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 27</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod28">159</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 28</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod29">160</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 29</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod30">161</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 30</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+</MSModSpecSet>\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae admin_scripts/species --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/species Sun May 31 09:05:57 2015 -0400 |
| b |
| b'@@ -0,0 +1,252 @@\n+>Fungi\r\n+Ashbya gossypii\tagossypii_eg_gene\r\n+Aspergillus clavatus\taclavatus_eg_gene\r\n+Aspergillus flavus\taflavus_eg_gene\r\n+Aspergillus fumigatus\tafumigatus_eg_gene\r\n+Aspergillus fumigatusa1163\tafumigatusa1163_eg_gene\r\n+Aspergillus nidulans\tanidulans_eg_gene\r\n+Aspergillus niger\taniger_eg_gene\r\n+Aspergillus oryzae\taoryzae_eg_gene\r\n+Aspergillus terreus\taterreus_eg_gene\r\n+Blumeria graminis\tbgraminis_eg_gene\r\n+Botrytis cinerea\tbcinerea_eg_gene\r\n+Colletotrichum gloeosporioides\tcgloeosporioides_eg_gene\r\n+Colletotrichum higginsianum\tchigginsianum_eg_gene\r\n+Colletotrichum orbiculare\tcorbiculare_eg_gene\r\n+Cryptococcus neoformans\tcneoformans_eg_gene\r\n+Dothistroma septosporum\tdseptosporum_eg_gene\r\n+Fusarium fujikuroi\tffujikuroi_eg_gene\r\n+Fusarium graminearum\tfgraminearum_eg_gene\r\n+Fusarium oxysporum\tfoxysporum_eg_gene\r\n+Fusarium pseudograminearum\tfpseudograminearum_eg_gene\r\n+Fusarium solani\tfsolani_eg_gene\r\n+Fusarium verticillioides\tfverticillioides_eg_gene\r\n+Gaeumannomyces graminis\tggraminis_eg_gene\r\n+Colletotrichum graminicola\tcgraminicola_eg_gene\r\n+Komagataella pastoris\tkpastoris_eg_gene\r\n+Leptosphaeria maculans\tlmaculans_eg_gene\r\n+Magnaporthe oryzae\tmoryzae_eg_gene\r\n+Magnaporthe poae\tmpoae_eg_gene\r\n+Melampsora larici-populina\tmlaricipopulina_eg_gene\r\n+Neosartorya fischeri\tnfischeri_eg_gene\r\n+Neurospora crassa\tncrassa_eg_gene\r\n+Phaeosphaeria nodorum\tpnodorum_eg_gene\r\n+Puccinia graminis\tpgraminis_eg_gene\r\n+Puccinia graminis Ug99\tpgraminisug99_eg_gene\r\n+Puccinia triticina\tptriticina_eg_gene\r\n+Pyrenophora teres\tpteres_eg_gene\r\n+Pyrenophora tritici-repentis\tptriticirepentis_eg_gene\r\n+Saccharomyces cerevisiae\tscerevisiae_eg_gene\r\n+Schizosaccharomyces cryophilus\tscryophilus_eg_gene\r\n+Schizosaccharomyces japonicus\tjaponicus_eg_gene\r\n+Schizosaccharomyces octosporus\toctosporus_eg_gene\r\n+Schizosaccharomyces pombe\tspombe_eg_gene\r\n+Sclerotinia sclerotiorum\tssclerotiorum_eg_gene\r\n+Sporisorium reilianum\tsreilianum_eg_gene\r\n+Trichoderma reesei\ttreesei_eg_gene\r\n+Trichoderma virens\ttvirens_eg_gene\r\n+Tuber melanosporum\ttmelanosporum_eg_gene\r\n+Ustilago maydis\tumaydis_eg_gene\r\n+Verticillium dahliae JR2\tvdahliaejr2_eg_gene\r\n+Verticillium dahliae\tdahliae_eg_gene\r\n+Yarrowia lipolytica\tylipolytica_eg_gene\r\n+Zymoseptoria tritici\tztritici_eg_gene\r\n+\r\n+>Metazoa\r\n+Acyrthosiphon pisum\tapisum_eg_gene\r\n+Aedes aegypti (Yellow fever mosquito)\taaegypti_eg_gene\r\n+Amphimedon queenslandica\taqueenslandica_eg_gene\r\n+Anopheles darlingi\tadarlingi_eg_gene\r\n+Anopheles gambiae (African malaria mosquito) \tagambiae_eg_gene\r\n+Apis mellifera \tamellifera_eg_gene\r\n+Atta cephalotes \tacephalotes_eg_gene\r\n+Bombyx mori \tbmori_eg_gene\r\n+Brugia malayi \tbmalayi_eg_gene\r\n+Caenorhabditis brenneri \tcbrenneri_eg_gene\r\n+Caenorhabditis briggsae \tcbriggsae_eg_gene\r\n+Caenorhabditis elegans \tcelegans_eg_gene\r\n+Caenorhabditis japonica \tcjaponica_eg_gene\r\n+Caenorhabditis remanei \tcremanei_eg_gene\r\n+Culex quinquefasciatus (Southern house mosquito) \tcquinquefasciatus_eg_gene\r\n+Danaus plexippus \tdplexippus_eg_gene\r\n+Daphnia pulex \tdpulex_eg_gene\r\n+Dendroctonus ponderosae\tponderosae_eg_gene\r\n+Drosophila ananassae \tdananassae_eg_gene\r\n+Drosophila erecta \tderecta_eg_gene\r\n+Drosophila grimshawi \tdgrimshawi_eg_gene\r\n+Drosophila melanogaster (Fruit fly) \tdmelanogaster_eg_gene\r\n+Drosophila mojavensis \tdmojavensis_eg_gene\r\n+Drosophila persimilis \tdpersimilis_eg_gene\r\n+Drosophila pseudoobscura \tdpseudoobscura_eg_gene\r\n+Drosophila sechellia \tdsechellia_eg_gene\r\n+Drosophila simulans \tdsimulans_eg_gene\r\n+Drosophila virilis \tdvirilis_eg_gene\r\n+Drosophila willistoni \tdwillistoni_eg_gene\r\n+Drosophila yakuba \tdyakuba_eg_gene\r\n+Heliconius melpomene \thmelpomene_eg_gene\r\n+Helobdella robusta\trobusta_eg_gene\r\n+Ixodes scapularis (Black-legged tick) \tiscapularis_eg_gene\r\n+Loa loa \tlloa_eg_gene\r\n+Lottia gigantea\tlgigantea_eg_gene\r\n+Megaselia scalaris \tmscalaris_eg_gene\r\n+Melitaea cinxia\tmcinxia_eg_gene\r\n+Mnemiopsis leidyi\tmleidyi_eg_gene\r\n+Nasonia vitripennis \tnvitripennis_eg_gene\r\n+Nematostella vectensis \tnv'..b'um\tpultimum_eg_gene\r\n+Pythium vexans\tpvexans_eg_gene\r\n+Tetrahymena thermophila\ttthermophila_eg_gene\r\n+Thalassiosira pseudonana\ttpseudonana_eg_gene\r\n+Toxoplasma gondii\ttgondii_eg_gene\r\n+Trypanosoma brucei\ttbrucei_eg_gene\r\n+\r\n+>Vertebrates\r\n+Alpaca (Vicugna pacos)\tvpacos_gene_ensembl\r\n+Amazon molly (Poecilia formosa)\tpformosa_gene_ensembl\r\n+Anole lizard (Anolis carolinensis)\tacarolinensis_gene_ensembl\r\n+Armadillo (Dasypus novemcinctus)\tdnovemcinctus_gene_ensembl\r\n+Bushbaby (Otolemur garnettii)\togarnettii_gene_ensembl\r\n+C. elegans (Caenorhabditis elegans)\tcelegans_gene_ensembl\r\n+C.intestinalis (Ciona intestinalis)\tcintestinalis_gene_ensembl\r\n+C.savignyi (Ciona savignyi)\tcsavignyi_gene_ensembl\r\n+Cat (Felis catus)\tfcatus_gene_ensembl\r\n+Cave fish (Astyanax mexicanus)\tamexicanus_gene_ensembl\r\n+Chicken (Gallus gallus)\tggallus_gene_ensembl\r\n+Chimpanzee (Pan troglodytes)\tptroglodytes_gene_ensembl\r\n+Chinese softshell turtle (Pelodiscus sinensis)\tpsinensis_gene_ensembl\r\n+Cod (Gadus morhua)\tgmorhua_gene_ensembl\r\n+Coelacanth (Latimeria chalumnae)\tlchalumnae_gene_ensembl\r\n+Cow (Bos taurus)\tbtaurus_gene_ensembl\r\n+Dog (Canis lupus familiaris)\tcfamiliaris_gene_ensembl\r\n+Dolphin (Tursiops truncatus)\tttruncatus_gene_ensembl\r\n+Duck (Anas platyrhynchos)\taplatyrhynchos_gene_ensembl\r\n+Elephant (Loxodonta africana)\tlafricana_gene_ensembl\r\n+Ferret (Mustela putorius furo)\tmfuro_gene_ensembl\r\n+Flycatcher (Ficedula albicollis)\tfalbicollis_gene_ensembl\r\n+Fruitfly (Drosophila melanogaster)\tdmelanogaster_gene_ensembl\r\n+Fugu (Takifugu rubripes)\ttrubripes_gene_ensembl\r\n+Gibbon (Nomascus leucogenys)\tnleucogenys_gene_ensembl\r\n+Gorilla (Gorilla gorilla gorilla)\tggorilla_gene_ensembl\r\n+Guinea Pig (Cavia porcellus)\tcporcellus_gene_ensembl\r\n+Hedgehog (Erinaceus europaeus)\teeuropaeus_gene_ensembl\r\n+Horse (Equus caballus)\tecaballus_gene_ensembl\r\n+Human (Homo sapiens)\thsapiens_gene_ensembl\r\n+Hyrax (Procavia capensis)\tpcapensis_gene_ensembl\r\n+Kangaroo rat (Dipodomys ordii)\tdordii_gene_ensembl\r\n+Lamprey (Petromyzon marinus)\tpmarinus_gene_ensembl\r\n+Lesser hedgehog tenrec (Echinops telfairi)\tetelfairi_gene_ensembl\r\n+Macaque (Macaca mulatta)\tmmulatta_gene_ensembl\r\n+Marmoset (Callithrix jacchus)\tcjacchus_gene_ensembl\r\n+Medaka (Oryzias latipes)\tolatipes_gene_ensembl\r\n+Megabat (Pteropus vampyrus)\tpvampyrus_gene_ensembl\r\n+Microbat (Myotis lucifugus)\tmlucifugus_gene_ensembl\r\n+Mouse (Mus musculus)\tmmusculus_gene_ensembl\r\n+Mouse Lemur (Microcebus murinus)\tmmurinus_gene_ensembl\r\n+Opossum (Monodelphis domestica)\tmdomestica_gene_ensembl\r\n+Orangutan (Pongo abelii)\tpabelii_gene_ensembl\r\n+Panda (Ailuropoda melanoleuca)\tamelanoleuca_gene_ensembl\r\n+Pig (Sus scrofa)\tsscrofa_gene_ensembl\r\n+Pika (Ochotona princeps)\toprinceps_gene_ensembl\r\n+Platyfish (Xiphophorus maculatus)\txmaculatus_gene_ensembl\r\n+Platypus (Ornithorhynchus anatinus)\toanatinus_gene_ensembl\r\n+Rabbit (Oryctolagus cuniculus)\tocuniculus_gene_ensembl\r\n+Rat (Rattus norvegicus)\trnorvegicus_gene_ensembl\r\n+S. cerevisiae (Saccharomyces cerevisiae)\tscerevisiae_gene_ensembl\r\n+Sheep (Ovis aries)\toaries_gene_ensembl\r\n+Shrew (Sorex araneus)\tsaraneus_gene_ensembl\r\n+Sloth (Choloepus hoffmanni)\tchoffmanni_gene_ensembl\r\n+Spotted gar (Lepisosteus oculatus)\tloculatus_gene_ensembl\r\n+Squirrel (Ictidomys tridecemlineatus)\titridecemlineatus_gene_ensembl\r\n+Stickleback (Gasterosteus aculeatus)\tgaculeatus_gene_ensembl\r\n+Tarsier (Tarsius syrichta)\ttsyrichta_gene_ensembl\r\n+Tasmanian devil (Sarcophilus harrisii)\tsharrisii_gene_ensembl\r\n+Tetraodon (Tetraodon nigroviridis)\ttnigroviridis_gene_ensembl\r\n+Tilapia (Oreochromis niloticus)\toniloticus_gene_ensembl\r\n+Tree Shrew (Tupaia belangeri)\ttbelangeri_gene_ensembl\r\n+Turkey (Meleagris gallopavo)\tmgallopavo_gene_ensembl\r\n+Vervet-AGM (Chlorocebus sabaeus)\tcsabaeus_gene_ensembl\r\n+Wallaby (Macropus eugenii)\tmeugenii_gene_ensembl\r\n+Xenopus (Xenopus tropicalis)\txtropicalis_gene_ensembl\r\n+Zebra Finch (Taeniopygia guttata)\ttguttata_gene_ensembl\r\n+Zebrafish (Danio rerio)\tdrerio_gene_ensembl\n\\ No newline at end of file\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -0,0 +1,105 @@ +<macros> + <xml name="stdio"> + <stdio> + <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"/> + </stdio> + </xml> + <token name="@GENERAL_PARAMETERS@"> + -frag_tol "${fragment_tol}" + -prec_tol "${precursor_ion_tol}" + -prec_ppm "${precursor_ion_tol_units}" + -enzyme "${enzyme}" + #set $fixed_mods_str = $fixed_modifications or '' + #set $variable_mods_str = $variable_modifications or '' + #if $fixed_mods_str + -fixed_mods "$fixed_mods_str" + #end if + #if $variable_mods_str + -variable_mods "$variable_mods_str" + #end if + -min_charge $min_charge + -max_charge $max_charge + -mc $missed_cleavages + -fi $forward_ion + -ri $reverse_ion + </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"> + <option value="1">Parts per million (ppm)</option> + <option value="2">Daltons</option> + </param> + <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" + help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> + <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" + help="Provide error value for fragment ions, based on instrument used"/> + <param name="enzyme" type="select" label="Enzyme" + help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Formic Acid">Formic Acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C, no P rule">Lys-C, no P rule</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Trypsin + CNBr">Trypsin + CNBr</option> + <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> + <option value="Trypsin, no P rule">Trypsin, no P rule</option> + <option value="whole protein">whole protein</option> + <option value="Asp-N">Asp-N</option> + <option value="Glu-C">Glu-C</option> + <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> + <option value="Top-Down">Top-Down</option> + <option value="Semi-Tryptic">Semi-Tryptic</option> + <option value="No enzyme">No enzyme</option> + <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> + <option value="Asp-N (DE)">Asp-N (DE)</option> + <option value="Glu-C (DE)">Glu-C (DE)</option> + <option value="Lys-N (K)">Lys-N (K)</option> + <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> + <option value="Semi-Glu-C">Semi-Glu-C</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" + help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> + <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> + <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> + <option value="a">a</option> + <option value="b" selected="true">b</option> + <option value="c">c</option> + </param> + <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> + <option value="x">x</option> + <option value="y" selected="true">y</option> + <option value="z">z</option> + </param> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1186/1471-2105-12-70</citation> + <citation type="doi">10.1002/pmic.201000595</citation> + <citation type="doi">doi:10.1038/nbt.3109</citation> + </citations> + </xml> + +</macros> |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae peptide_shaker.xml --- a/peptide_shaker.xml Wed Jun 25 11:50:38 2014 -0400 +++ b/peptide_shaker.xml Sun May 31 09:05:57 2015 -0400 |
| [ |
| b'@@ -1,211 +1,44 @@\n-<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0">\n+<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0">\n <description>\n- Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.\n+ Perform protein identification using various search engines based on results from SearchGUI\n </description>\n <requirements>\n- <requirement type="package" version="0.31.4">peptide_shaker</requirement>\n- <requirement type="package" version="1.19.5">searchgui</requirement>\n- <!--<requirement type="package" version="2.2.29">blast+</requirement>-->\n+ <requirement type="package" version="0.38">peptide_shaker</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1:" level="fatal" description="Job Failed" />\n- <regex match="java.*Exception" level="fatal" description="Java Exception"/> \n- <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>\n- </stdio>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="stdio" />\n <command>\n-\n+<![CDATA[\n #from datetime import datetime\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 = \'macs2_stderr\'\n+ #set $temp_stderr = "peptideshaker_stderr"\n \n- mkdir output;\n mkdir output_reports;\n cwd=`pwd`;\n- #for $mgf in $peak_lists:\n- #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"\n- ln -s \'${mgf}\' \'${input_name}\';\n- #end for\n- ##ln -s "${input_database}" input_database.fasta;\n- cp "${input_database}" input_database.fasta;\n \n- ###########################################\n- #### Creating decoy database ####\n- ###########################################\n- #if $create_decoy:\n- echo "Creating decoy database.";\n- java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -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- #end if\n-\n- #####################################################\n- ## generate IdentificationParameters for SearchGUI ##\n- #####################################################\n-\n- (java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI\n- -out SEARCHGUI_IdentificationParameters.parameters\n- -prec_ppm "${precursor_ion_tol_units}"\n- -prec_tol "${precursor_ion_tol}"\n- -frag_tol "${fragment_tol}"\n- -enzyme "${enzyme}"\n- #set $fixed_mods_str = $fixed_modifications or \'\'\n- #set $variable_mods_str = $variable_modifications or \'\'\n- #if $fixed_mods_str\n- -fixed_mods "${fixed_mods_str}" \n- #end if\n- #if $variable_mods_str\n- -variable_mods "${variable_mods_str}"\n- #end if\n- -min_charge "${min_charge}"\n- -max_charge "${max_charge}"\n- -mc "${missed_cleavages}"\n- -fi "${forward_ion}"\n- -ri "${reverse_ion}"\n- -db input_database.fasta\n-\n- #if $advanced.advanced_type_selector == "advanced":\n-\n- #if $advanced.xtandem.xtandem_selector == "yes"\n-\n- -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}\n- -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}\n- -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}\n- -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}\n- '..b'value="no"/>\n <param name="filtering_options_selector" value="no"/>\n- <!--param name="xtandem_selector" value="no"/>-->\n- <param name="xtandem_selector" value="yes"/>\n- <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>\n-\n- <param name="omssa_selector" value="no"/>\n- <param name="msgf_selector" value="yes"/>\n- <param name="ms_amanda_selector" value="no"/>\n- \n- <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> \n+ <param name="outputs" value="zip,cps,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_zip"/>\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+ <param name="outputs" value="0,1,2,3,4,5,6,7"/>\n+ <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/>\n+ <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />\n+ <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />\n+ <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />\n+ <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />\n+ <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />\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_zip"/>\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@@ -814,8 +600,8 @@\n ----------\n \n * Protein(s): Protein(s) to which the peptide can be attached\n-* Sequence:\t Sequence of the peptide\n-* Variable Modifications:\tThe variable modifications\n+* Sequence: Sequence of the peptide\n+* Variable Modifications: The variable modifications\n * D-score:\t D-score for variable PTM localization\n * probabilistic PTM score:\tThe probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.\n * Localization Confidence:\tThe confidence in variable PTM localization.\n@@ -945,8 +731,6 @@\n * Validation:\tIndicates the validation level of the protein group.\n \n \n-\n-\n ------\n \n **Citation**\n@@ -955,4 +739,5 @@\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 </help>\n+ <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae repository_dependencies.xml --- a/repository_dependencies.xml Wed Jun 25 11:50:38 2014 -0400 +++ b/repository_dependencies.xml Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Required proteomics dependencies."> - <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d1ea609e57d4" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae searchgui.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui.xml Sun May 31 09:05:57 2015 -0400 |
| [ |
| b'@@ -0,0 +1,365 @@\n+<tool id="search_gui" name="Search GUI" version="1.27.0">\n+ <description>\n+ Perform protein identification using various search engines and prepare results for input to Peptide Shaker\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="1.27">searchgui</requirement>\n+ </requirements>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="stdio" />\n+ <command>\n+<![CDATA[\n+ #from datetime import datetime\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+\n+ mkdir output;\n+ mkdir output_reports;\n+ cwd=`pwd`;\n+ #for $mgf in $peak_lists:\n+ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"\n+ ln -s -f \'${mgf}\' \'${input_name}\';\n+ #end for\n+ ##ln -s "${input_database}" input_database.fasta;\n+ cp "${input_database}" input_database.fasta;\n+\n+ ###########################################\n+ #### Creating decoy database ####\n+ ###########################################\n+ #if $create_decoy:\n+ echo "Creating decoy database.";\n+ java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -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+ #end if\n+\n+ #####################################################\n+ ## generate IdentificationParameters for SearchGUI ##\n+ #####################################################\n+\n+ (java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI\n+ -out SEARCHGUI_IdentificationParameters.parameters\n+\n+ @GENERAL_PARAMETERS@\n+\n+ -db input_database.fasta\n+\n+ #if $advanced.advanced_type_selector == "advanced":\n+\n+ #if $advanced.xtandem.xtandem_selector == "yes"\n+\n+ -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}\n+ -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}\n+ -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}\n+ -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}\n+ -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}\n+\n+ #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"\n+ -xtandem_refine 1\n+ -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}\n+ -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}\n+ -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}\n+ -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}\n+ -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}\n+ #end if\n+ #end if\n+\n+ #if $advanced.omssa.omssa_selector == "yes"\n+ -omssa_hitlist_length ${advanced.omssa.hitlist_length}\n+ -omssa_remove_prec ${advanced.omssa.remove_precursor}\n+ -omssa_scale_prec ${advanced.omssa.scale_precursor}\n+ -omssa_estimate_charge ${advanced.omssa.estimate_charge}\n+ #end if\n+\n+ #if $advanced.msgf.msgf_selector == "yes"\n+ -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}\n+ -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}\n+ -msgf_termini ${advanced.'..b'ches will take much longer if selecting a value other than 2">\n+ <option value="0">0 (ie non-specific cleavage)</option>\n+ <option value="1">1 (ie semi-tryptic cleavage)</option>\n+ <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>\n+ </param>\n+ <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="myrimatch">\n+ <param name="myrimatch_selector" type="select" label="Run MyriMatch search">\n+ <option value="yes" selected="True">Search with MyriMatch</option>\n+ <option value="no">No MyriMatch search</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ </when>\n+ </conditional>\n+\n+ <conditional name="comet">\n+ <param name="comet_selector" type="select" label="Run Comet search">\n+ <option value="yes" selected="True">Search with Comet</option>\n+ <option value="no">No Comet search</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ </when>\n+ </conditional>\n+\n+ <conditional name="ms_amanda">\n+ <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">\n+ <option value="yes">Search with MS Amanda</option>\n+ <option value="no" selected="True">No MS Amanda search</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ </when>\n+ </conditional>\n+\n+ <conditional name="tide">\n+ <param name="tide_selector" type="select" label="Run Tide search">\n+ <option value="yes">Search with Tide</option>\n+ <option value="no" selected="True">No Comet search</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ </when>\n+ </conditional>\n+\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>\n+ <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>\n+ <param name="precursor_ion_tol" value="100"/>\n+ <param name="fixed_modifications" value="carbamidomethyl c"/>\n+ <param name="variable_modifications" value="oxidation of m"/>\n+ <param name="min_charge" value="1"/>\n+ <param name="max_charge" value="3"/>\n+ <param name="advanced_type_selector" value="advanced"/>\n+ <param name="xtandem_selector" value="yes"/>\n+ <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>\n+ <param name="omssa_selector" value="no"/>\n+ <param name="msgf_selector" value="yes"/>\n+ <param name="ms_amanda_selector" value="no"/>\n+ <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> \n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+Runs multiple search engines on any number of MGF peak lists using the SearchGUI.\n+\n+By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run.\n+\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/._tinyoutput.cps |
| b |
| Binary file test-data/._tinyoutput.cps has changed |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_certificate_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_certificate_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -0,0 +1,68 @@ +Project Details1: PeptideShaker Version: 0.37.4-beta +2: Date: Sat Feb 14 20:04:49 CET 2015 +3: Experiment: Galaxy_Experiment_2015021420041423940686 +4: Sample: Sample_2015021420041423940686 +5: Replicate Number: 1 +6: Identification Algorithms: X!Tandem and MS-GF+ +Database Search Parameters + +1: Precursor Accuracy 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: +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 +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: A-score: No +2: Accounting for Neutral Losses: No +3: False Location Rate: 1.0 +Spectrum Counting Parameters + +1: Method: NSAF +2: Validated Matches Only: Yes +Annotation Settings + +1: Intensity Limit: 0.75 +2: Automatic Annotation: Yes +3: Selected Ions: b, y +4: Neutral Losses: NH3, H2O +5: Neutral Losses Sequence Dependence: Yes +6: Selected Charges: 1, 2 +7: Fragment Ion m/z Tolerance: 0.5 |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_hierarchical_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_hierarchical_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| [ |
| b'@@ -0,0 +1,78 @@\n+\tMain Accession\tDescription\tMW [kDa]\tCoverage [%]\tPossible Coverage [%]\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\t3757.96\t92.52\t0.014450915311500504\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\t39\t39\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\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\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+1.1.1\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\ttinyspectra.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+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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\ttinyspectra.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+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\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+1.2.1\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\ttinyspectra.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+1.2.2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.'..b' 31.94 EValue:4.0e-10\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+1.15.1\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, 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\t\t\ttinyspectra.mgf\tCmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2241966836996\t0\t2.5298047449054923\t0\t\t\t\t100.0\tDoubtful\n+1.15.2\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, 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\t\t\ttinyspectra.mgf\tCmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2241966836996\t0\t2.5298047449054923\t0\t\t\t\t100.0\tDoubtful\n+2\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91\t\t69.9696370486838\t325.2\t100.0\t0.0032520325203252032\t\t\t\t\tRelated Proteins\tcds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\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\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|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\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|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\t\t\ttinyspectra.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+2.1.2\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\t\t\ttinyspectra.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' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_peptides_phoshorylation_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites #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; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 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; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 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 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 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 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 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 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 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 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 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 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 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 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 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 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 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 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 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 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 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 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 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 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_peptides_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_peptides_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -0,0 +1,17 @@ + Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #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; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 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; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful +3 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 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful +4 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 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful +5 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 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful +6 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 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful +7 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 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful +8 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 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful +9 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 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful +10 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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful +11 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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful +12 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 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful +13 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 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful +14 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 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful +15 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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful +16 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 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_proteins_phoshorylation_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| [ |
| @@ -0,0 +1,3 @@ + Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible 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 3757.96 92.52 0.014450915311500504 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 39 39 100.0 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 325.2 100.0 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 |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_proteins_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_proteins_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| [ |
| @@ -0,0 +1,3 @@ + Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible 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 3757.96 92.52 0.014450915311500504 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 39 39 100.0 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 325.2 100.0 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 |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_psm_phoshorylation_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| [ |
| b'@@ -0,0 +1,42 @@\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\tISITTYEEEIEDLHATAR\t\t\ttinyspectra.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\t\t\t\t\t100.0\tDoubtful\n+2\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\ttinyspectra.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+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\t\t\ttinyspectra.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+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\tSLQAENEQLR\t\t\ttinyspectra.mgf\tCmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942146837\t0\t2.0632379154490605\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\ttinyspectra.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\tMEIITITNQLQR\t\t\ttinyspectra.mgf\tCmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864506836997\t0\t-3.233580283650776\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\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\tYESQLSQIR\t\t\ttinyspectra.mgf\tCmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669286837\t0\t7.00561302556395\t0\t\t\t\t\t\t\t\t100.0\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 '..b'alue: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\ttinyspectra.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+34\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\t\t\ttinyspectra.mgf\tCmpd 871, MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354586837\t0\t1.7038016610019715\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n+35\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1197, MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.0560846836997\t0\t5.228393373659577\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n+36\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\ttinyspectra.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+37\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\ttinyspectra.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+38\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\tKGDIIATVDEWGPVNR\t\t\ttinyspectra.mgf\tCmpd 582, MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n+39\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\ttinyspectra.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+40\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\ttinyspectra.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+41\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\tASLGMAAGVAGGIATK\t\t\ttinyspectra.mgf\tCmpd 357, MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336876837\t0\t-2.733506911277659\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_psm_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_result1.tabular Sun May 31 09:05:57 2015 -0400 |
| [ |
| b'@@ -0,0 +1,42 @@\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\tISITTYEEEIEDLHATAR\t\t\ttinyspectra.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+2\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\ttinyspectra.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+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\t\t\ttinyspectra.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+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\tSLQAENEQLR\t\t\ttinyspectra.mgf\tCmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942146837\t0\t2.0632379154490605\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\ttinyspectra.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\tMEIITITNQLQR\t\t\ttinyspectra.mgf\tCmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864506836997\t0\t-3.233580283650776\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\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\tYESQLSQIR\t\t\ttinyspectra.mgf\tCmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669286837\t0\t7.00561302556395\t0\t\t\t\t100.0\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\tNLLLDANKENGELK\t\t\ttinyspectra.mgf\tCmpd '..b'005882 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\ttinyspectra.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+34\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\t\t\ttinyspectra.mgf\tCmpd 871, MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354586837\t0\t1.7038016610019715\t0\t\t\t\t100.0\tDoubtful\n+35\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1197, MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.0560846836997\t0\t5.228393373659577\t0\t\t\t\t100.0\tDoubtful\n+36\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\ttinyspectra.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+37\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\ttinyspectra.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+38\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\tKGDIIATVDEWGPVNR\t\t\ttinyspectra.mgf\tCmpd 582, MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\t0\t\t\t\t100.0\tDoubtful\n+39\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\ttinyspectra.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+40\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\ttinyspectra.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+41\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\tASLGMAAGVAGGIATK\t\t\ttinyspectra.mgf\tCmpd 357, MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336876837\t0\t-2.733506911277659\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_psm_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_psm_result2.tabular Sun May 31 09:05:57 2015 -0400 |
| [ |
| b'@@ -0,0 +1,42 @@\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\tISITTYEEEIEDLHATAR\t\t\ttinyspectra.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+2\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\ttinyspectra.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+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\t\t\ttinyspectra.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+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\tSLQAENEQLR\t\t\ttinyspectra.mgf\tCmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942146837\t0\t2.0632379154490605\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\ttinyspectra.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\tMEIITITNQLQR\t\t\ttinyspectra.mgf\tCmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864506836997\t0\t-3.233580283650776\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\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\tYESQLSQIR\t\t\ttinyspectra.mgf\tCmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669286837\t0\t7.00561302556395\t0\t\t\t\t100.0\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\tNLLLDANKENGELK\t\t\ttinyspectra.mgf\tCmpd '..b'005882 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\ttinyspectra.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+34\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\t\t\ttinyspectra.mgf\tCmpd 871, MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354586837\t0\t1.7038016610019715\t0\t\t\t\t100.0\tDoubtful\n+35\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1197, MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.0560846836997\t0\t5.228393373659577\t0\t\t\t\t100.0\tDoubtful\n+36\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\ttinyspectra.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+37\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\ttinyspectra.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+38\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\tKGDIIATVDEWGPVNR\t\t\ttinyspectra.mgf\tCmpd 582, MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\t0\t\t\t\t100.0\tDoubtful\n+39\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\ttinyspectra.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+40\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\ttinyspectra.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+41\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\tASLGMAAGVAGGIATK\t\t\ttinyspectra.mgf\tCmpd 357, MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336876837\t0\t-2.733506911277659\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_result1.cps |
| b |
| Binary file test-data/peptide_shaker_result1.cps has changed |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/peptide_shaker_result1.zip |
| b |
| Binary file test-data/peptide_shaker_result1.zip has changed |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/searchgui_tinydb1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_tinydb1.fasta Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -0,0 +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 +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 +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 +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 +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 +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 +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 +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 +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 +MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF +>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 +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 +FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/searchgui_tinyspectra1.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_tinyspectra1.mgf Sun May 31 09:05:57 2015 -0400 |
| b |
| b'@@ -0,0 +1,6153 @@\n+BEGIN IONS\r\n+TITLE= Cmpd 636, +MSn(730.3981), 66.9 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IONS\r\n+\r\n' |
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| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/tiny_searchgui_result1.zip |
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| Binary file test-data/tiny_searchgui_result1.zip has changed |
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| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/tinydb.fasta --- a/test-data/tinydb.fasta Wed Jun 25 11:50:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ ->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 -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 -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 -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 -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 -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 -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 -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 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->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 -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 -FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/tinyoutput.cps |
| b |
| Binary file test-data/tinyoutput.cps has changed |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae test-data/tinyspectra.mgf --- a/test-data/tinyspectra.mgf Wed Jun 25 11:50:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6153 +0,0 @@\n-BEGIN IONS\r\n-TITLE= Cmpd 636, +MSn(730.3981), 66.9 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IONS\r\n-\r\n' |
| b |
| diff -r 7e61179c5952 -r 2cafc729b2ae tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 25 11:50:38 2014 -0400 +++ b/tool_dependencies.xml Sun May 31 09:05:57 2015 -0400 |
| b |
| @@ -1,12 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="1.19.5"> - <repository changeset_revision="e544ffa7ea6f" name="package_searchgui_1_19" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="1.27"> + <repository changeset_revision="6ad0463c0e64" name="package_searchgui_1_27" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="0.31.4"> - <repository changeset_revision="45ee9e65471f" name="package_peptideshaker_0_31" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="0.38"> + <repository changeset_revision="958037b48c33" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <!--<package name="blast+" version="2.2.29"> - <repository name="package_blast_plus_2_2_29" owner="iuc" /> - </package>--> </tool_dependency> |