annotate sanitize_bed.py @ 4:f95f403841ad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
author iuc
date Mon, 22 Jun 2020 07:29:41 -0400
parents
children 584beffa972b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
2
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
3 import sys
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
4
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
5
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
6 with open(sys.argv[1]) as i:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
7 bed_data = i.readlines()
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
8
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
9 sanitized_data = []
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
10 try:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
11 for record in bed_data:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
12 fields = record.split('\t')
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
13 sanitized_data.append(
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
14 '\t'.join(fields[:4] + ['60'] + fields[5:])
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
15 )
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
16 except IndexError:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
17 pass # leave column number issue to getmasked
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
18 else:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
19 with open(sys.argv[1], 'w') as o:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
diff changeset
20 o.writelines(sanitized_data)