Mercurial > repos > rliterman > csp2

comparison CSP2/bin/saveSNPDiffs.py @ 28:893a6993efe3

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 13:48:13 -0500
parents 792274118b2e
children 93393808f415
comparison
equal deleted inserted replaced
27:792274118b2e 28:893a6993efe3
28 28
29 parser = argparse.ArgumentParser() 29 parser = argparse.ArgumentParser()
30 parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file") 30 parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file")
31 parser.add_argument("--summary_file", help="Path to the summary file") 31 parser.add_argument("--summary_file", help="Path to the summary file")
32 parser.add_argument("--isolate_file", help="Path to the isolate data file") 32 parser.add_argument("--isolate_file", help="Path to the isolate data file")
33 parser.add_argument('--trim_name', type=str, default="", help='trim name') 33 parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
34 parser.add_argument("--ref_id_file", help="Path to the reference IDs file") 34 parser.add_argument("--ref_id_file", help="Path to the reference IDs file")
35 args = parser.parse_args() 35 args = parser.parse_args()
36 36
37 snpdiffs_list_file = args.snpdiffs_file 37 snpdiffs_list_file = args.snpdiffs_file
38 summary_file = args.summary_file 38 summary_file = args.summary_file