Mercurial > repos > rliterman > csp2

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author rliterman
date Wed, 04 Dec 2024 13:48:13 -0500
parents 792274118b2e
children
comparison
equal deleted inserted replaced
27:792274118b2e 28:893a6993efe3
9 parser = argparse.ArgumentParser(description='Fetch Reads') 9 parser = argparse.ArgumentParser(description='Fetch Reads')
10 parser.add_argument('--read_dir', type=str, help='path to directory containing read files') 10 parser.add_argument('--read_dir', type=str, help='path to directory containing read files')
11 parser.add_argument('--read_filetype',default='fastq.gz', type=str, help='read filetype information') 11 parser.add_argument('--read_filetype',default='fastq.gz', type=str, help='read filetype information')
12 parser.add_argument('--forward_suffix',default='_1.fastq.gz', type=str, help='forward suffix') 12 parser.add_argument('--forward_suffix',default='_1.fastq.gz', type=str, help='forward suffix')
13 parser.add_argument('--reverse_suffix',default = '_2.fastq.gz', type=str, help='reverse suffix') 13 parser.add_argument('--reverse_suffix',default = '_2.fastq.gz', type=str, help='reverse suffix')
14 parser.add_argument('--trim_name', type=str, default="", help='trim name') 14 parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
15 args = parser.parse_args() 15 args = parser.parse_args()
16 16
17 # Get path to directory containing read files 17 # Get path to directory containing read files
18 read_dir = os.path.abspath(args.read_dir) 18 read_dir = os.path.abspath(args.read_dir)
19 if not os.path.isdir(read_dir): 19 if not os.path.isdir(read_dir):