Mercurial > repos > glogobyte > mirviz

comparison viz.py @ 12:847318ed9a5c draft

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author glogobyte
date Wed, 20 Oct 2021 15:17:24 +0000
parents 0a4d6c483ff0
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11:0a4d6c483ff0 12:847318ed9a5c
6 6
7 ################################################################################################################################################################################################################################################################## 7 ##################################################################################################################################################################################################################################################################
8 starttime = time.time() 8 starttime = time.time()
9 9
10 parser = argparse.ArgumentParser() 10 parser = argparse.ArgumentParser()
11 parser.add_argument("-in", "--input", help="choose type of analysis", action="store") 11 parser.add_argument("-in", "--input", help="input file from Deseq2 or EdgeR", action="store")
12 parser.add_argument("-p_value", "--pval", help="choose type of analysis", action="store") 12 parser.add_argument("-p_value", "--pval", help="p-value or p-adj threshold", action="store")
13 parser.add_argument("-fc", "--log2fc", help="choose type of analysis", action="store") 13 parser.add_argument("-fc", "--log2fc", help="log2fc threshold", action="store")
14 parser.add_argument("-top", "--top_mirnas", help="choose type of analysis", action="store") 14 parser.add_argument("-top", "--top_mirnas", help="Top significant genes", action="store")
15 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store") 15 parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
16 parser.add_argument("-statistic", "--stat", help="tool directory path", action="store") 16 parser.add_argument("-statistic", "--stat", help="Filter option by p-value or p-adj or basemean (only for Deseq2)", action="store")
17 parser.add_argument("-diff_tool", "--tool", help="tool directory path", action="store") 17 parser.add_argument("-diff_tool", "--tool", help="Choose tool for Differential expression Deseq2 or EdgeR", action="store")
18 18
19 args = parser.parse_args() 19 args = parser.parse_args()
20 20
21 l=Lock() 21 l=Lock()
22 number = int(args.top_mirnas) 22 number = int(args.top_mirnas)