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APOSTL_Static_Bubblegraph_Generator.py |
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| diff -r 0489ece83d7f -r 66faf09e5e8e APOSTL_Static_Bubblegraph_Generator.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/APOSTL_Static_Bubblegraph_Generator.py Tue Mar 15 15:19:03 2016 -0400 |
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| @@ -0,0 +1,80 @@ +####################################################################################### +# 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)) + |