Mercurial > repos > bornea > saint_bubblebeam
view Bubblebeam_For_SAINT_wrapper.py @ 18:e992232032ae draft
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author | bornea |
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date | Fri, 20 Nov 2015 11:14:37 -0500 |
parents | b11a6884496e |
children | 7ce59d092bae |
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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] #r_path = sys.argv[16] #r_path = str(r_path) + r"bin/" if crapome == "None": crapome = "FALSE" if label == "false": label = "FALSE" elif label == "true": label = "TRUE" cmd = str(ins_path) +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))