Mercurial > repos > bornea > prohits_dotplot_generator
view ProHits_DotPlot_Generator.py @ 16:89a7ee06257f draft
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author | bornea |
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date | Wed, 16 Mar 2016 12:10:43 -0400 |
parents | d458f5c875f1 |
children | c1017fb6bb0d |
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####################################################################################### # 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]))