Mercurial > repos > bornea > apostl_static_bubblegraph_generator
view APOSTL_Static_Bubblegraph_Generator.py @ 27:33e9cdd6bbe8 draft default tip
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author | bornea |
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date | Wed, 18 May 2016 16:57:02 -0400 |
parents | b712ed693d09 |
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####################################################################################### # 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] inter_file = sys.argv[4] main_x = sys.argv[5] main_y = sys.argv[6] size_id = sys.argv[7] color = sys.argv[8] SS_cutoff = sys.argv[9] FC_cutoff = sys.argv[10] NS_cutoff = sys.argv[11] theme = sys.argv[12] label = sys.argv[13] label_color = sys.argv[14] bubble_color = sys.argv[15] outline_color = sys.argv[16] filt_color = sys.argv[17] outfile = sys.argv[18] ins_path = sys.argv[19] if crapome == "None": crapome = "FALSE" if color == "None": color = "Tan" if theme == "None": theme = "Default" if label_color == "None": label_color = "black" if bubble_color == "None": bubble_color = "Alizarin crimson" if outline_color == "None": outline_color = "black" if filt_color == "None": filt_color = "tan" if main_x == "lnNSAF": main_x = "\"ln(NSAF)\"" if main_y == "lnNSAF": main_y = "\"ln(NSAF)\"" if size_id == "lnNSAF": size_id = "\"ln(NSAF)\"" if main_x == "log2FoldChange": main_x = "\"log2(FoldChange)\"" if main_y == "log2FoldChange": main_y = "\"log2(FoldChange)\"" if size_id == "log2FoldChange": size_id = "\"log2(FoldChange)\"" if main_x == "logOddsScore": main_x = "\"log(OddsScore)\"" if main_y == "logOddsScore": main_y = "\"log(OddsScore)\"" if size_id == "logOddsScore": size_id = "\"log(OddsScore)\"" cmd = (r"Rscript "+ str(ins_path) + r"/Static_Bubble_Plot_Cmdln.R " + str(list_file) + r" " + str(prey_file) + r" " + str(crapome) + r" " + str(inter_file) + r" " + str(main_x) + r" " + str(main_y) + r" " + str(size_id) + r" " + str(color) + r" " + str(SS_cutoff) + r" " + str(FC_cutoff) + r" " + str(NS_cutoff) + r" " + str(theme) + r" " + str(label) + r" " + str(label_color) + r" " + str(bubble_color) + r" " + str(outline_color) + r" " + str(filt_color)) os.system(cmd) open('./BubbleGraph.png') os.rename('BubbleGraph.png', str(outfile))