comparison saint_wrapper.py @ 26:bb1601260366 draft

Uploaded

26:bb1601260366

#######################################################################################
# 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)