| Previous changeset 4:496d9565eb28 (2016-03-15) Next changeset 6:66faf09e5e8e (2016-03-15) |
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Commit message:
Uploaded |
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added:
test_files/MQ_crapome.txt test_files/MQ_prey.txt test_files/SAINT_list_MQ.txt |
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removed:
APOSTL_Static_Bubblegraph_Generator.py APOSTL_Static_Bubblegraph_Generator.xml GNU Free Documentation License.txt bubbles_v9_NSAF_natural_log.R tool_dependencies.xml |
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| diff -r 496d9565eb28 -r 0489ece83d7f APOSTL_Static_Bubblegraph_Generator.py --- a/APOSTL_Static_Bubblegraph_Generator.py Tue Mar 15 15:11:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,80 +0,0 @@ -####################################################################################### -# Python-code: Bubblebeam wrapper -# Author: Adam L Borne -# Contributers: Paul A Stewart, Brent Kuenzi -####################################################################################### -# This program runs the R script that generates a bubble plot. Python script simply -# handles arguments and interacts with Galaxy. -####################################################################################### -# Copyright (C) Adam Borne. -# Permission is granted to copy, distribute and/or modify this document -# under the terms of the GNU Free Documentation License, Version 1.3 -# or any later version published by the Free Software Foundation; -# with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. -# A copy of the license is included in the section entitled "GNU -# Free Documentation License". -####################################################################################### -## REQUIRED INPUT ## - -# 1) list_file: SaintExpress output file. -# 2) prey_file: Prey file listing gene name, sequence legnth, and gene id. -# 3) crapome: Crapome file can be created at http://crapome.org. (default = "None") -# 4) color: Fill color of the bubbles, if set to crapome it shades based on crapome -# potential. (default = "Red") -# 5) cutoff: Lower limit saint score for generating bubble plot. (default = 0.8) -# 6) mq_sc: MQ for MaxQuant data and SC for Scaffold data. -# 7) inc_file: List of uniprot ids to be used exclusively. (default = "None") -# 8) exc_file: List of uniprot ids to be excluded from plot. (default = "None") -####################################################################################### - -import os -import sys -import time - - -list_file = sys.argv[1] -prey_file = sys.argv[2] -crapome = sys.argv[3] -color = sys.argv[4] -label = sys.argv[5] -cutoff = sys.argv[6] -mq_sc = sys.argv[7] -inc_file = sys.argv[8] -exc_file = sys.argv[9] -output_file_name = sys.argv[10] -bub_zoom_NSAF = sys.argv[11] -bub_zoom_SAINT =sys.argv[12] -bub_SAINT = sys.argv[13] -bub_NSAF = sys.argv[14] -ins_path = sys.argv[15] - -if crapome == "None": - crapome = "FALSE" - - -if label == "false": - label = "FALSE" -elif label == "true": - label = "TRUE" - -cmd = (r"Rscript "+ str(ins_path) + r"/bubbles_v9_NSAF_natural_log.R " + str(list_file) + r" " - + str(prey_file) + r" " + str(crapome) + r" " + str(color) + r" " + str(label) + r" " - + str(cutoff) + r" " + str(mq_sc) + r" " + str(inc_file) + r" " + str(exc_file)) -os.system(cmd) -time.sleep(3) - -open('./output.txt') -os.rename('output.txt', str(output_file_name)) - -open('./bubble_zoom_NSAF.png') -os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF)) - -open('./bubble_zoom_SAINT.png') -os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT)) - -open('./bubble_SAINT.png') -os.rename('bubble_SAINT.png', str(bub_SAINT)) - -open('./bubble_NSAF.png') -os.rename('bubble_NSAF.png', str(bub_NSAF)) - |
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| diff -r 496d9565eb28 -r 0489ece83d7f APOSTL_Static_Bubblegraph_Generator.xml --- a/APOSTL_Static_Bubblegraph_Generator.xml Tue Mar 15 15:11:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,131 +0,0 @@ -<tool id="APOSTL_Static_Bubblegraph_Generator" name="APOSTL Static Bubblegraph Generator"> - <description></description> - <command interpreter="python">APOSTL_Static_Bubblegraph_Generator.py $list_file $prey_file $crapome $color $label $cutoff $type $inc_file $exc_file $outfile $NSAF_zoom $SAINT_zoom $SAINT $NSAF \$INSTALL_RUN_PATH/</command> - <requirements> - <requirement type="set_environment">INSTALL_RUN_PATH</requirement> - </requirements> - <inputs> - <param type="select" name="type" label="MaxQuant or Scaffold"> - <option value="MQ">MaxQuant</option> - <option value="SC">Scaffold</option> - </param> - <param format="txt" name="list_file" type="data" label="List File"/> - <param format="txt" name="prey_file" type="data" label="Prey File"/> - <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/> - <param name="color" type="select" label="Color" optional="true"> - <option value="crapome">Crapome</option> - <option value="red">Red</option> - <option value="blue">Blue</option> - </param> - <param type="boolean" name="label" checked="true" label="Use Labels"/> - <param type="float" name="cutoff" label="SAINT Score Cutoff" help="Select a value between 0 and 1 written like 0.8." value="0.8"/> - <param format="txt" name="inc_file" type="data" label="List of Uniprot IDs to Include" optional="true"/> - <param format="txt" name="exc_file" type="data" label="List of Uniprot IDs to Exclude" optional="true"/> - </inputs> - <outputs> - <data format="txt" name="outfile" label="Outfile"/> - <data format="png" name="NSAF_zoom" label="Zoom NSAF" /> - <data format="png" name="SAINT_zoom" label="Zoom SAINT" /> - <data format="png" name="NSAF" label="NSAF" /> - <data format="png" name="SAINT" label="SAINT" /> - </outputs> - <stdio> - <regex match="error" - source="stdout" - level="fatal" - description="Unknown error"/> - </stdio> - - <tests> - <test> - <param name="input" value="fa_gc_content_input.fa"/> - <output name="out_file1" file="fa_gc_content_output.txt"/> - </test> - </tests> - <help> -Post-processing: -Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things: - -APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait - -OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome - -Bubble graphs are generated for each bait where: - -- x axis is the natural log of the NSAF values - -- y axis is the observed log2 fold change (as compared to control) - -- bubble radius is proportional to the average observed spectra - -OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan - -APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option. - -INPUTS: - -List File: - -- SAINTexpress generated "list.txt" file - -Prey File: - -- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress - -Crapome File: - -- raw output from Crapome Workflow 1 query (http://www.crapome.org) - -Color: - -- Specify the color of the bubbles within the graph. - -- If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity - -Use labels: - -- Adds gene name labels to bubbles within the "zoomed in" graphs -SAINT Score Cutoff: - -- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8) - -- Also used for filtering during the generation of the cytoscape network - -Species: - -- Human, mouse, or yeast - -Interaction Confidence: - -- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database - -- Suggestions: - -* low: 0 - -* medium: 0.5 - -* high: 0.7 - -* very high: 0.9 - -OUTPUTS: - -Bubble Graphs: - -- Unfiltered Data: - -* NSAF v. Log2(FoldChange) - -* SAINTscore v. Log2(FoldChange) - -- Filtered by SAINT Score - -* NSAF v. Log2(FoldChange) - -* SAINTscore v. Log2(FoldChange) - -Output.txt -- SAINTexpress "list.txt" output with additional columns that were used during the analysis - </help> -</tool> |
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| diff -r 496d9565eb28 -r 0489ece83d7f GNU Free Documentation License.txt --- a/GNU Free Documentation License.txt Tue Mar 15 15:11:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,451 +0,0 @@\n-\r\n- GNU Free Documentation License\r\n- Version 1.3, 3 November 2008\r\n-\r\n-\r\n- Copyright (C) 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc.\r\n- <http://fsf.org/>\r\n- Everyone is permitted to copy and distribute verbatim copies\r\n- of this license document, but changing it is not allowed.\r\n-\r\n-0. PREAMBLE\r\n-\r\n-The purpose of this License is to make a manual, textbook, or other\r\n-functional and useful document "free" in the sense of freedom: to\r\n-assure everyone the effective freedom to copy and redistribute it,\r\n-with or without modifying it, either commercially or noncommercially.\r\n-Secondarily, this License preserves for the author and publisher a way\r\n-to get credit for their work, while not being considered responsible\r\n-for modifications made by others.\r\n-\r\n-This License is a kind of "copyleft", which means that derivative\r\n-works of the document must themselves be free in the same sense. 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| diff -r 496d9565eb28 -r 0489ece83d7f bubbles_v9_NSAF_natural_log.R --- a/bubbles_v9_NSAF_natural_log.R Tue Mar 15 15:11:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,233 +0,0 @@\n-rm(list=ls())\r\n-###################################################################################################\r\n-# R-code: Multi-bubble graph generation from SAINTexpress output\r\n-# Author: Brent Kuenzi\r\n-###################################################################################################\r\n-library(dplyr); library(tidyr); library(ggplot2)\r\n-###################################################################################################\r\n-### Run program ###\r\n-\r\n-## REQUIRED INPUT ##\r\n-# 1) listfile: SAINTexpress generated "list.txt" file\r\n-# 2) preyfile: SAINT pre-processing generated "prey.txt" file used to run SAINTexpress\r\n-## OPTIONAL INPUT ##\r\n-# 3) crapome: raw output from crapome Workflow 1 query (http://www.crapome.org)\r\n-# 4) color: bubble color (default = "red")\r\n-# - color= "crapome": color bubbles based on Crapome(%)\r\n-# - Also recognizes any color within R\'s built-in colors() vector\r\n-# 5) label: Adds gene name labels to bubbles within the "zoomed in" graphs (default = FALSE)\r\n-# 6) cutoff: Saintscore cutoff to be assigned for filtering the "zoomed in" graphs (default = 0.8)\r\n-###################################################################################################\r\n-main <- function(listfile, preyfile , crapome=FALSE, color="red", label=FALSE, cutoff=0.8, type="SC", inc_file = "None", exc_file = "None" ) {\r\n- cutoff_check(cutoff)\r\n- listfile <- list_type(listfile, inc_file, exc_file)\r\n- if(type == "SC") {\r\n- df <- merge_files_sc(listfile, preyfile, crapome)\r\n- }\r\n- if(type == "MQ") {\r\n- df <- merge_files_mq(listfile, preyfile, crapome)\r\n- }\r\n- bubble_NSAF(df,color)\r\n- bubble_SAINT(df,color)\r\n- bubble_zoom_SAINT(df, color, label, cutoff)\r\n- bubble_zoom_NSAF(df, color, label, cutoff)\r\n- write.table(df,"output.txt",sep="\\t",quote=FALSE, row.names=FALSE)\r\n-}\r\n-\r\n-list_type <- function(df, inc_file, exc_file) {\r\n- Saint <- read.delim(df, stringsAsFactors=FALSE)\r\n- if (inc_file != "None") {\r\n- if (exc_file == "None"){\r\n- inc_prots <- read.delim(inc_file, sep=\'\\t\', header=FALSE, stringsAsFactors=FALSE)\r\n- filtered_df = subset(Saint, Saint$Prey == inc_prots[,1])\r\n- }\r\n- else {\r\n- inc_prots <- read.delim(inc_file, sep=\'\\t\', header=FALSE, stringsAsFactors=FALSE)\r\n- exc_prots <- read.delim(exc_file, sep=\'\\t\', header=FALSE, stringsAsFactors=FALSE)\r\n- filtered_df = subset(Saint, Saint$Prey == inc_prots[,1])\r\n- filtered_df = subset(filtered_df, filtered_df$Prey != exc_prots[,1])\r\n- }\r\n- }\r\n- else if (exc_file != "None") {\r\n- exc_prots <- read.delim(exc_file, sep=\'\\t\', header=FALSE, stringsAsFactors=FALSE)\r\n- filtered_df = subset(Saint, Saint$Prey != exc_prots[,1])\r\n- }\r\n- else {\r\n- filtered_df = Saint\r\n- }\r\n- return(filtered_df)\r\n- \r\n-}\r\n-###################################################################################################\r\n-# Merge input files and caculate Crapome(%) and NSAF for each protein for each bait\r\n-###################################################################################################\r\n-merge_files_mq <- function(SAINT, prey_DF, crapome=FALSE) {\r\n- #SAINT <- read.table(SAINT_DF, sep=\'\\t\', header=TRUE)\r\n- prey <- read.table(prey_DF, sep=\'\\t\', header=FALSE); colnames(prey) <- c("Prey", "Length", "PreyGene")\r\n- DF <- merge(SAINT,prey)\r\n- DF$SpecSum <- log2(DF$SpecSum)\r\n- \r\n- if(crapome!=FALSE) {\r\n- crapome <- read.table(crapome, sep=\'\\t\', header=TRUE)\r\n- colnames(crapome) <- c("Prey", "Symbol", "Num.of.Exp", "Ave.SC", "Max.SC")\r\n- DF1 <- merge(DF, crapome); as.character(DF1$Num.of.Exp); DF1$Symbol <- NULL;\r\n- DF1$Ave.SC <- NULL; DF1$Max.SC <- NULL #remove unnecessary columns\r\n- DF1$Num.of.Exp <- sub("^$", "0 / 1", DF1$Num.of.Exp ) #replace blank values with 0 / 1\r\n- DF <- DF1 %>% separate(Num.of.Exp, c("NumExp", "TotalExp"), " / ") #split into 2 columns\r\n- DF$CrapomePCT <- 100 - (as.integer(DF$NumExp) / as.integer(D'..b'ecSum) +\r\n- scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score") + \r\n- geom_point(aes(x=SaintScore,y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)\r\n- if(label==TRUE & length(a$NSAF!=0)) {\r\n- p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)\r\n- }\r\n- if(length(levels(data$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}\r\n- return(ggsave(p, width=8,height=4,filename = "bubble_zoom_SAINT.png"))\r\n- }\r\n-}\r\n-###################################################################################################\r\n-# Filter proteins on Saintscore cutoff and plot for each bait x=log(NSAF), y=Log2(FoldChange)\r\n-###################################################################################################\r\n-bubble_zoom_NSAF <- function(data, color, label=FALSE, cutoff=0.8) {\r\n- if(color=="crapome") {\r\n- a <- subset(data, CrapomePCT <80 & SaintScore>=cutoff, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait, PreyGene))\r\n- b <- subset(data, CrapomePCT >=80 & SaintScore >=cutoff, select = c(NSAF,SpecSum, CrapomePCT, FoldChange, SaintScore, Bait, PreyGene))\r\n- p <- qplot(x=log(NSAF), y=log2(FoldChange), data=a, colour=I("tan"),size=SpecSum) + \r\n- scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score") + \r\n- geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a)\r\n- if(label==TRUE & length(a$NSAF!=0)) {\r\n- p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black")\r\n- }\r\n- if(length(levels(a$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}\r\n- p <- p + geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum, color=CrapomePCT), data=b) + \r\n- scale_colour_gradient(limits=c(80, 100), low="tan", high="red") + \r\n- labs(colour="CRAPome Probability \\nof Specific Interaction (%)", x="ln(NSAF)") + \r\n- geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=b)\r\n- if(label==TRUE & length(b$NSAF!=0)) {\r\n- p <- p + geom_text(data=b, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)\r\n- }\r\n- return(ggsave(p, width=8,height=4,filename = "bubble_zoom_NSAF.png"))\r\n- }\r\n- if(color != "crapome") {\r\n- a <- subset(data, SaintScore>=cutoff, select = c(NSAF,SpecSum, FoldChange, SaintScore, Bait, PreyGene))\r\n- p <- qplot(x=log(NSAF), y=log2(FoldChange), data=a, colour=I(color), size=SpecSum) +\r\n- scale_size(range=c(1,10)) + ggtitle("Filtered on SAINT score") + \r\n- geom_point(aes(x=log(NSAF),y=log2(FoldChange), size=SpecSum), colour="black", shape=21, data=a) + \r\n- labs(x="ln(NSAF)")\r\n- if(label==TRUE & length(a$NSAF!=0)) {\r\n- p <- p + geom_text(data=a, aes(label=PreyGene, size=10, vjust=0, hjust=0),colour="black", show_guide=FALSE)\r\n- }\r\n- if(length(levels(data$Bait) > 1)) {p <- p + facet_wrap(~Bait, scales="free_y")}\r\n- return(ggsave(p, width=8,height=4,filename = "bubble_zoom_NSAF.png"))\r\n- }\r\n-}\r\n-###################################################################################################\r\n-# Check Saintscore cutoff and stop program if not between 0 and 1\r\n-###################################################################################################\r\n-cutoff_check <- function(cutoff){\r\n- if( any(cutoff < 0 | cutoff > 1) ) stop(\'SAINT score cutoff not between 0 and 1. Please correct and try again\')\r\n-}\r\n-\r\n-args <- commandArgs(trailingOnly = TRUE)\r\n-main(args[1],args[2],args[3],args[4],args[5],args[6],args[7],args[8],args[9])\r\n-\r\n-#main("test_list.txt", "preytest.txt", crapome="craptest.txt", color="crapome", label=TRUE)\r\n-#main("Crizo_list.txt", "prey_cr.txt", crapome = "crizo_crap.txt", color="crapome", label=TRUE, cutoff=0.7)\r\n-#main("test_list.txt", "preytest.txt", crapome=FALSE, color="magenta", label=FALSE, cutoff=1.1)\n\\ No newline at end of file\n' |
| b |
| diff -r 496d9565eb28 -r 0489ece83d7f test_files/MQ_crapome.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/MQ_crapome.txt Tue Mar 15 15:18:16 2016 -0400 |
| b |
| b'@@ -0,0 +1,575 @@\n+User Input\tMapped Gene Symbol\tNum of Expt. (found/total)\tAve SC\tMax SC\n+Q8WVM8\tSCFD1\t17 / 411\t1.5\t4\n+Q13049\tTRIM32\t1 / 411\t1\t1\n+P35232\tPHB\t85 / 411\t3.9\t34\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P09382\tLGALS1\t40 / 411\t4.8\t27\n+P07900\tHSP90AA1\t272 / 411\t30\t327\n+P04259\tKRT6B\t319 / 411\t22.1\t320\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+Q96P48\tARAP1\t1 / 411\t1\t1\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P18433\tInvalid identifier / gene not available\t\t\t\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+P42338\tInvalid identifier / gene not available\t\t\t\n+Q96NH3\tInvalid identifier / gene not available\t\t\t\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P33992\tMCM5\t100 / 411\t5\t34\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+O95831\tAIFM1\t101 / 411\t7.8\t92\n+O00567\tNOP56\t96 / 411\t5.9\t50\n+P57088\tTMEM33\t34 / 411\t1.9\t6\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+O15482\tInvalid identifier / gene not available\t\t\t\n+P05109\tS100A8\t57 / 411\t3.1\t17\n+P42338\tInvalid identifier / gene not available\t\t\t\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+O60716\tCTNND1\t32 / 411\t4.6\t26\n+P07437\tTUBB\t382 / 411\t37.5\t338\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P42704\tLRPPRC\t130 / 411\t15.5\t112\n+P07900\tHSP90AA1\t272 / 411\t30\t327\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+O95831\tAIFM1\t101 / 411\t7.8\t92\n+P38646\tHSPA9\t307 / 411\t19\t160\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+Q8TEM1\tNUP210\t25 / 411\t5.9\t24\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+Q15751\tHERC1\t1 / 411\t1\t1\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+A5A3E0\tPOTEF\t351 / 411\t11.2\t193\n+P68366\tTUBA4A\t377 / 411\t28.6\t242\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+Q99615\tDNAJC7\t59 / 411\t2.9\t10\n+P82930\tMRPS34\t24 / 411\t1.9\t6\n+P35568\tInvalid identifier / gene not available\t\t\t\n+REV__Q8WX94\tInvalid identifier / gene not available\t\t\t\n+P31948\tSTIP1\t120 / 411\t8.6\t58\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+CON__P02533\tInvalid identifier / gene not available\t\t\t\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+P0DMV8\tInvalid identifier / gene not available\t\t\t\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P12236\tSLC25A6\t201 / 411\t7\t119\n+P05141\tSLC25A5\t223 / 411\t7.1\t58\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+Q8WUY1\tTHEM6\t4 / 411\t1.8\t3\n+REV__Q6IE37\tInvalid identifier / gene not available\t\t\t\n+Q9UBL6\tCPNE7\t19 / 411\t1.6\t5\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+P49411\tTUFM\t139 / 411\t8.6\t53\n+P08581\tInvalid identifier / gene not available\t\t\t\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P43246\tMSH2\t45 / 411\t3\t27\n+P82930\tMRPS34\t24 / 411\t1.9\t6\n+Q8NEG7\tDENND6B\t2 / 411\t1\t1\n+P62258\tYWHAE\t186 / 411\t9.4\t90\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+Q92552\tMRPS27\t31 / 411\t2.6\t9\n+P42338\tInvalid identifier / gene not available\t\t\t\n+Q14451\tGRB7\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+Q02978\tSLC25A11\t55 / 411\t3.1\t18\n+REV__Q0VFZ6\tInvalid identifier / gene not available\t\t\t\n+Q07889\tSOS1\t1 / 411\t1\t1\n+P22681\tCBL\t2 / 411\t1.5\t2\n+Q05639\tEEF1A2\t343 / 411\t13.4\t175\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+P52735\tVAV2\t1 / 411\t1\t1\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q4G1C9\tInvalid identifier / gene not available\t\t\t\n+P21860\tInvalid identifier / gene not available\t\t\t\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q8NFI3\tENGASE\t2 / 411\t1\t1\n+Q14571\tITPR2\t5 / 411\t4.4\t10\n+P42224\tSTAT1\t23 / 411\t4.7\t19\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P05141\tSLC25A5\t223 / 411\t7.1\t58\n+Q75V66\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P0CG4'..b'\n+CON__Q5D862\tInvalid identifier / gene not available\t\t\t\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P46109\tCRKL\t33 / 411\t7.7\t25\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P49368\tCCT3\t165 / 411\t15.1\t114\n+Q14451\tGRB7\t1 / 411\t1\t1\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+Q53GQ0\tHSD17B12\t27 / 411\t1.9\t7\n+P25705\tATP5A1\t210 / 411\t11\t83\n+Q15084\tPDIA6\t129 / 411\t6.7\t52\n+P35568\tInvalid identifier / gene not available\t\t\t\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+O00329\tPIK3CD\t1 / 411\t1\t1\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P18433\tInvalid identifier / gene not available\t\t\t\n+O95782\tAP2A1\t24 / 411\t2.4\t14\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+Q71U36\tTUBA1A\t389 / 411\t34.9\t299\n+P0CG48\tUBC\t233 / 411\t6.5\t90\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+Q8NF37\tLPCAT1\t7 / 411\t1.4\t4\n+CON__P35527\tInvalid identifier / gene not available\t\t\t\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+REV__E9PKD4\tInvalid identifier / gene not available\t\t\t\n+CON__P35527\tInvalid identifier / gene not available\t\t\t\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P40763\tSTAT3\t36 / 411\t6\t25\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+P11142\tHSPA8\t396 / 411\t39.2\t332\n+Q06124\tPTPN11\t41 / 411\t3.5\t36\n+Q13946\tInvalid identifier / gene not available\t\t\t\n+Q92569\tPIK3R3\t4 / 411\t1.3\t2\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P25205\tMCM3\t120 / 411\t6.6\t63\n+Q9Y4H2\tIRS2\t4 / 411\t1.3\t2\n+P62266\tRPS23\t160 / 411\t4.7\t28\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__P00761\tInvalid identifier / gene not available\t\t\t\n+P21860\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+CON__P00761\tInvalid identifier / gene not available\t\t\t\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+REV__Q6ZU80\tInvalid identifier / gene not available\t\t\t\n+Q07021\tC1QBP\t223 / 411\t11.4\t381\n+P17066\tHSPA6\t380 / 411\t14.1\t159\n+Q92859\tInvalid identifier / gene not available\t\t\t\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P62805\tHIST4H4\t225 / 411\t13.6\t316\n+P13639\tEEF2\t207 / 411\t14.5\t219\n+CON__ENSEMBL:ENSBTAP00000016242\tInvalid identifier / gene not available\t\t\t\n+P43304\tGPD2\t3 / 411\t2\t4\n+P07900\tHSP90AA1\t272 / 411\t30\t327\n+P18433\tInvalid identifier / gene not available\t\t\t\n+REV__Q8WXI4\tInvalid identifier / gene not available\t\t\t\n+CON__P02533\tInvalid identifier / gene not available\t\t\t\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+P35030\tPRSS3\t61 / 411\t3.6\t38\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P21860\tInvalid identifier / gene not available\t\t\t\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P18433\tInvalid identifier / gene not available\t\t\t\n+P25705\tATP5A1\t210 / 411\t11\t83\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P29353\tSHC1\t9 / 411\t1.6\t3\n+P42338\tInvalid identifier / gene not available\t\t\t\n+Q92569\tPIK3R3\t4 / 411\t1.3\t2\n+Q8NF91\tSYNE1\t10 / 411\t1.2\t2\n+Q3BBV2\tInvalid identifier / gene not available\t\t\t\n+P38646\tHSPA9\t307 / 411\t19\t160\n+P14923\tJUP\t109 / 411\t7.7\t46\n+P11021\tHSPA5\t360 / 411\t16.9\t112\n+P11802\tCDK4\t27 / 411\t2.4\t28\n+CON__P13645\tInvalid identifier / gene not available\t\t\t\n+P68871\tHBB\t56 / 411\t2.1\t9\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+Q06124\tPTPN11\t41 / 411\t3.5\t36\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P04259\tKRT6B\t319 / 411\t22.1\t320\n+P04264\tKRT1\t386 / 411\t79.5\t1178\n+P35908\tKRT2\t356 / 411\t44.6\t629\n+P42338\tInvalid identifier / gene not available\t\t\t\n+P42336\tPIK3CA\t1 / 411\t1\t1\n+P62993\tGRB2\t7 / 411\t1.4\t3\n+P05141\tSLC25A5\t223 / 411\t7.1\t58\n+P15924\tDSP\t126 / 411\t19.4\t237\n+P52735\tVAV2\t1 / 411\t1\t1\n+CON__P02662\tInvalid identifier / gene not available\t\t\t\n+Q9Y4H2\tIRS2\t4 / 411\t1.3\t2\n+P07437\tTUBB\t382 / 411\t37.5\t338\n+Q13509\tInvalid identifier / gene not available\t\t\t\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P63173\tRPL38\t139 / 411\t9\t58\n+Q12774\tARHGEF5\t1 / 411\t1\t1\n+O00459\tPIK3R2\t6 / 411\t2.2\t7\n+P00533\tEGFR\t16 / 411\t4.3\t15\n+P18433\tInvalid identifier / gene not available\t\t\t\n' |
| b |
| diff -r 496d9565eb28 -r 0489ece83d7f test_files/MQ_prey.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/MQ_prey.txt Tue Mar 15 15:18:16 2016 -0400 |
| b |
| @@ -0,0 +1,292 @@ +Q8WVM8 642 SCFD1 +Q13049 653 TRIM32 +P35232 272 PHB +O00459 728 PIK3R2 +P09382 135 LGALS1 +P07900 732 HSP90AA1 +Q14568 343 HSP90AA2 +P08238 724 HSP90AB1 +Q58FF8 381 HSP90AB2P +P04259 564 KRT6B +P02538 564 KRT6A +P48668 564 KRT6C +P04264 644 KRT1 +Q96P48 1450 ARAP1 +Q12774 1597 ARHGEF5 +P18433 802 PTPRA +Q07021 282 C1QBP +P42338 1070 PIK3CB +Q96NH3 1257 TBC1D32 +P33992 734 MCM5 +P11021 654 HSPA5 +P13645 584 KRT10 +O95831 613 AIFM1 +O00567 594 NOP56 +P57088 247 TMEM33 +O95782 977 AP2A1 +O94973 939 AP2A2 +O15482 410 TEX28 +P05109 93 S100A8 +O60716 968 CTNND1 +P07437 444 TUBB +P42704 1394 LRPPRC +P38646 679 HSPA9 +P35908 639 KRT2 +Q01546 638 KRT76 +P19013 534 KRT4 +P11142 646 HSPA8 +P54652 639 HSPA2 +Q8TEM1 1887 NUP210 +P62993 217 GRB2 +P00533 1210 EGFR +Q15751 4861 HERC1 +P68363 451 TUBA1B +Q71U36 451 TUBA1A +Q13748 450 TUBA3C +Q6PEY2 450 TUBA3E +Q9NY65 449 TUBA8 +P68366 448 TUBA4A +A5A3E0 1075 POTEF +P0CG38 1075 POTEI +Q6S8J3 1075 POTEE +P68032 377 ACTC1 +P68133 377 ACTA1 +P60709 375 ACTB +P63261 375 ACTG1 +Q9BYX7 375 POTEKP +P62736 377 ACTA2 +P63267 376 ACTG2 +Q9BQE3 449 TUBA1C +Q99615 494 DNAJC7 +P82930 218 MRPS34 +P35568 1242 IRS1 +Q8WX94 980 NLRP7 +P31948 543 STIP1 +Q7Z3Y7 464 KRT28 +Q7Z3Y8 459 KRT27 +Q7Z3Z0 450 KRT25 +P02533 472 KRT14 +O00329 1044 PIK3CD +P12236 298 SLC25A6 +P05141 298 SLC25A5 +P42336 1068 PIK3CA +Q8WUY1 208 THEM6 +Q6IE37 1185 OVOS1 +Q9UBL6 633 CPNE7 +Q9HCH3 593 CPNE5 +Q86YQ8 564 CPNE8 +O95741 557 CPNE6 +Q96A23 557 CPNE4 +Q8IYJ1 553 CPNE9 +Q96FN4 548 CPNE2 +O75131 537 CPNE3 +P49411 452 TUFM +P08581 1390 MET +P43246 934 MSH2 +Q8NEG7 585 DENND6B +P62258 255 YWHAE +P31947 248 SFN +P61981 247 YWHAG +Q04917 246 YWHAH +P63104 245 YWHAZ +P27348 245 YWHAQ +Q92552 414 MRPS27 +Q14451 532 GRB7 +Q02978 314 SLC25A11 +Q0VFZ6 552 CCDC173 +Q07889 1333 SOS1 +Q07890 1332 SOS2 +P22681 906 CBL +Q05639 463 EEF1A2 +P68104 462 EEF1A1 +Q5VTE0 462 EEF1A1P5 +P52735 878 VAV2 +Q4G1C9 344 GLIPR1L2 +P21860 1342 ERBB3 +Q8NFI3 743 ENGASE +Q14571 2701 ITPR2 +P42224 750 STAT1 +Q75V66 913 ANO5 +P0CG48 685 UBC +P0CG47 229 UBB +P62979 156 RPS27A +P62987 128 UBA52 +P29353 583 SHC1 +Q7Z794 578 KRT77 +Q86Y46 540 KRT73 +P12035 628 KRT3 +Q9NSB2 600 KRT84 +Q7RTS7 529 KRT74 +Q3SY84 523 KRT71 +Q14CN4 511 KRT72 +O95678 551 KRT75 +Q5XKE5 535 KRT79 +P05787 483 KRT8 +P13647 590 KRT5 +P08729 469 KRT7 +Q06124 597 PTPN11 +P17066 643 HSPA6 +P48741 367 HSPA7 +P53680 142 AP2S1 +P69905 142 HBA1 +P40763 770 STAT3 +A6NK06 481 IRG1 +Q86WR7 435 PROSER2 +P02768 609 ALB +P78527 4128 PRKDC +P35527 623 KRT9 +P04626 1255 ERBB2 +O00264 195 PGRMC1 +P12235 298 SLC25A4 +P43304 727 GPD2 +Q8NDL9 886 AGBL5 +P68371 445 TUBB4B +Q13885 445 TUBB2A +Q9BVA1 445 TUBB2B +Q13509 450 TUBB3 +Q06830 199 PRDX1 +Q13162 271 PRDX4 +P46109 303 CRKL +P07355 339 ANXA2 +A6NMY6 339 ANXA2P2 +Q9GZT3 109 SLIRP +P62249 146 RPS16 +P14678 240 SNRPB +Q8TD57 4116 DNAH3 +Q58FF7 597 HSP90AB3P +Q9Y2R5 130 MRPS17 +Q58FG0 334 HSP90AA5P +P98077 582 SHC2 +Q99611 448 SEPHS2 +P11802 303 CDK4 +P08779 473 KRT16 +Q9NS86 450 LANCL2 +P61978 463 HNRNPK +Q15366 365 PCBP2 +Q13191 982 CBLB +Q4G0P3 5121 HYDIN +Q6P1M0 643 SLC27A4 +P51648 485 ALDH3A2 +P13646 458 KRT13 +Q8IXB1 793 DNAJC10 +P04350 444 TUBB4A +P62269 152 RPS18 +P62829 140 RPL23 +P10809 573 HSPD1 +Q14116 193 IL18 +Q5T9A4 648 ATAD3B +Q9NVI7 634 ATAD3A +Q5T2N8 411 ATAD3C +P08727 400 KRT19 +P05783 430 KRT18 +P0CG39 1038 POTEJ +O43196 834 MSH5 +P63173 70 RPL38 +Q6URK8 271 TEPP +Q99456 494 KRT12 +P19012 456 KRT15 +Q04695 432 KRT17 +A6NNZ2 444 NA +Q3ZCM7 444 TUBB8 +Q9H4B7 451 TUBB1 +Q9NP72 206 RAB18 +Q86SQ7 713 SDCCAG8 +Q2M243 656 CCDC27 +Q96K76 1375 USP47 +Q15165 354 PON2 +Q9BYK8 2649 HELZ2 +Q16543 378 CDC37 +Q8WXH0 6885 SYNE2 +Q9UJM3 462 ERRFI1 +O00461 696 GOLIM4 +Q05655 676 PRKCD +A1L190 88 SYCE3 +P16144 1822 ITGB4 +O95816 211 BAG2 +Q99623 299 PHB2 +Q5JWF2 1037 GNAS +P63092 394 GNAS +P38405 381 GNAL +P04899 355 GNAI2 +A8MTJ3 354 GNAT3 +P08754 354 GNAI3 +P09471 354 GNAO1 +P19087 354 GNAT2 +P63096 354 GNAI1 +P11488 350 GNAT1 +Q92569 461 PIK3R3 +Q8NF37 534 LPCAT1 +Q6Y7W6 1299 GIGYF2 +P49757 651 NUMB +Q9Y6R0 609 NUMBL +P37235 193 HPCAL1 +P61601 193 NCALD +P84074 193 HPCA +Q53GA4 152 PHLDA2 +Q63ZY3 851 KANK2 +Q6PIJ6 1188 FBXO38 +Q15257 358 PPP2R4 +Q96BR5 231 COA7 +P14923 745 JUP +P35222 781 CTNNB1 +Q8IV45 518 UNC5CL +Q86VU5 262 COMTD1 +Q9C0F3 470 ZNF436 +Q69YG0 159 TMEM42 +O94808 682 GFPT2 +Q03989 594 ARID5A +P30825 629 SLC7A1 +Q9NU02 776 ANKEF1 +Q9UBF8 816 PI4KB +Q9BWG4 385 SSBP4 +Q9Y6F6 885 MRVI1 +Q96JB1 4490 DNAH8 +P06702 114 S100A9 +Q99575 1024 POP1 +Q9H069 523 LRRC48 +P60953 191 CDC42 +Q03001 7570 DST +Q9UPN3 7388 MACF1 +Q5VZP5 1158 DUSP27 +A6NCF5 533 KLHL33 +A6NMZ7 2263 COL6A6 +P35498 2009 SCN1A +Q9BWN1 585 PRR14 +Q8IWK6 1321 GPR125 +P27986 724 PIK3R1 +Q6NUN0 579 ACSM5 +P68871 147 HBB +Q8WV24 401 PHLDA1 +Q9HCY8 104 S100A14 +Q6PKX4 331 DOK6 +O15440 1437 ABCC5 +O75592 4640 MYCBP2 +P61626 148 LYZ +P11274 1271 BCR +Q12979 859 ABR +Q8IW35 865 CEP97 +Q5D862 2391 FLG2 +P49368 545 CCT3 +Q53GQ0 312 HSD17B12 +P25705 553 ATP5A1 +Q15084 440 PDIA6 +E9PKD4 350 NPIPA5 +Q13946 482 PDE7A +P25205 808 MCM3 +Q9Y4H2 1338 IRS2 +P62266 143 RPS23 +Q6ZU80 1094 CEP128 +Q92859 1461 NEO1 +P62805 103 HIST1H4A +P13639 858 EEF2 +Q58FF6 505 HSP90AB4P +Q8WXI4 607 ACOT11 +P35030 304 PRSS3 +Q15303 1308 ERBB4 +Q8NF91 8797 SYNE1 +Q3BBV2 869 NBPF8 +Q86T75 865 NBPF11 +Q7Z3Y9 468 KRT26 +P02042 147 HBD +Q9H0C2 315 SLC25A31 +P15924 2871 DSP |
| b |
| diff -r 496d9565eb28 -r 0489ece83d7f test_files/SAINT_list_MQ.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/SAINT_list_MQ.txt Tue Mar 15 15:18:16 2016 -0400 |
| b |
| b'@@ -0,0 +1,2337 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|
| b |
| diff -r 496d9565eb28 -r 0489ece83d7f tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 15 15:11:25 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable name="INSTALL_RUN_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> -</tool_dependency> \ No newline at end of file |