comparison sanitize_bed.py @ 11:5671e1d3d5ee draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
author iuc
date Wed, 13 Jul 2022 15:18:33 +0000
parents db536ad45f28
children
comparison
equal deleted inserted replaced
10:9f978da6528a 11:5671e1d3d5ee
7 bed_data = i.readlines() 7 bed_data = i.readlines()
8 8
9 sanitized_data = [] 9 sanitized_data = []
10 try: 10 try:
11 for record in bed_data: 11 for record in bed_data:
12 fields = record.split('\t') 12 if record.strip():
13 sanitized_data.append( 13 fields = record.split('\t')
14 '\t'.join(fields[:4] + ['60'] + fields[5:]) 14 sanitized_data.append(
15 ) 15 '\t'.join(fields[:4] + ['60'] + fields[5:])
16 )
16 except IndexError: 17 except IndexError:
17 pass # leave column number issue to getmasked 18 pass # leave column number issue to getmasked
18 else: 19 else:
19 with open(sys.argv[1], 'w') as o: 20 with open(sys.argv[1], 'w') as o:
20 o.writelines(sanitized_data) 21 o.writelines(sanitized_data)