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added:
saint_wrapper.py |
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| diff -r f6f472d55b35 -r bb1601260366 saint_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/saint_wrapper.py Thu Jan 28 16:31:19 2016 -0500 |
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| @@ -0,0 +1,92 @@ +####################################################################################### +# Python-code: SAINT wrapper +# Author: Adam L Borne +# Contributers: Paul A Stewart, Brent Kuenzi +####################################################################################### +# This program takes a bait, prey and interactions file and uses SaintExpress to +# generate resulting matrices. This allows the software to run within 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) inter_file: Interaction file listing experiment bait, assignement, gene name and +# spectrum count. +# 2) prey_file: Prey file listing gene name, sequence legnth, and gene id. +# 3) bait_file: Bait file listing bait experiment, assignment, and T or C. +# 4) vc_bool: Boolean used to determine if virtual controls are being used. +# 5) vc_num: Number of virtual controls to be used. (default = 1) +# 6) go_bool: Boolean used to determine used of external data set. +# 7) go_file: External data file if being used. (default = "None") +####################################################################################### +import os +import sys + +inter_file = sys.argv[1] +prey_file = sys.argv[2] +bait_file = sys.argv[3] +num_of_rep = sys.argv[4] +vc_bool = sys.argv[5] +vc_num = sys.argv[6] +go_bool = sys.argv[7] +go_file = sys.argv[8] +output_file = sys.argv[9] +ins_path = sys.argv[10] + +# Verifies the install of SaintExpress and installs if not found. +def first_run_check(): + os.chdir(ins_path) + dirs_list = [] + for (dirpath, dirnames, filename) in os.walk("./"): + dirs_list.extend(dirnames) + break + if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list: + pass + else: + cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip" + os.system(cmd) + os.chdir("./SAINTexpress_v3.6.1__2015-05-03") + cmd1 = r"make -j" + os.system(cmd1) + +def default_run(inter_file1,prey_file1,bait_file1,output_file1,num_of_rep1): + cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + +def with_L(inter_file1,prey_file1,bait_file1,output_file1,vc_num1,num_of_rep1): + cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + +def external_data_no_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1): + cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + +def external_data_with_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1,vc_num1): + cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1) + os.system(cmd) + open('list.txt') + os.rename('list.txt', str(output_file1)) + +first_run_check() +if (vc_bool == "true"): + if (go_bool == "false"): + with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep) + elif (go_bool == "true"): + external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num) +elif (vc_bool == "false"): + if (go_bool == "false"): + default_run(inter_file, prey_file, bait_file, output_file, num_of_rep) + elif (go_bool == "true"): + external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep) |