| Previous changeset 13:e74888e94f96 (2016-03-16) Next changeset 15:a6c081fcc0a9 (2016-03-16) |
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Commit message:
Uploaded |
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added:
ProHits_DotPlot_Generator.py |
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| diff -r e74888e94f96 -r d458f5c875f1 ProHits_DotPlot_Generator.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProHits_DotPlot_Generator.py Wed Mar 16 12:10:25 2016 -0400 |
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| @@ -0,0 +1,56 @@ +####################################################################################### +# Python-code: Dotplot Runner +# Author: Adam L Borne +# Contributers: Paul A Stewart, Brent Kuenzi +####################################################################################### +# This script runs the dotplot program found at http://prohitstools.mshri.on.ca/. +####################################################################################### +# 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) FDR1: Primary false discovery rate. (default = 0.01) +# 3) FDR2: Secondary false discovery rate. (default = 0.025) +# 4) spec_max: Maximum spectral count. (default = 50) +####################################################################################### + +import os +import sys + + +FDR1 = sys.argv[2] +FDR2 = sys.argv[3] +spec_max = sys.argv[4] +os.rename(sys.argv[1], "saint_input.txt") +ins_path = sys.argv[9] + +dirs_list = [] +for (dirpath, dirnames, filename) in os.walk(str(ins_path)): + dirs_list.extend(dirnames) + break +if r"Dotplot_Release" in dirs_list: + pass +else: + cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz" + os.system(cmd) + + +cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) + + r" -t " + str(FDR2) + " -m " + str(spec_max)) +os.system(cmd) + +cmd1 = r"cp -a ./Output_saint_input/. ." +os.system(cmd1) + +os.rename("saint_input.txt", str(sys.argv[1])) +os.rename('dotplot.pdf', str(sys.argv[5])) +os.rename('bait2bait.pdf', str(sys.argv[6])) +os.rename('estimated.pdf', str(sys.argv[7])) +os.rename('stats.pdf', str(sys.argv[8])) \ No newline at end of file |