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comparison CSP2/bin/fetchReads.py @ 27:792274118b2e

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 12:50:59 -0500
parents 01431fa12065
children 893a6993efe3
comparison
equal deleted inserted replaced
26:6f85641ecd48 27:792274118b2e
6 import argparse 6 import argparse
7 7
8 # Parse args 8 # Parse args
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', 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', 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', 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, help='trim name') 14 parser.add_argument('--trim_name', type=str, default="", 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):