Mercurial > repos > iuc > ivar_variants

annotate sanitize_bed.py @ 17:abbc8041e8ec draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 32fbe8a14173afe0b39f1483afaba958dc6cd027
author iuc
date Fri, 21 Jun 2024 15:20:59 +0000
parents 584beffa972b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
parents:
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1 #!/usr/bin/env python
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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3 import sys
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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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
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7 bed_data = i.readlines()
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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8
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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9 sanitized_data = []
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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10 try:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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11 for record in bed_data:
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584beffa972b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
iuc
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12 if record.strip():
584beffa972b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
iuc
parents: 4
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13 fields = record.split('\t')
584beffa972b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
iuc
parents: 4
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14 sanitized_data.append(
584beffa972b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
iuc
parents: 4
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15 '\t'.join(fields[:4] + ['60'] + fields[5:])
584beffa972b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
iuc
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16 )
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f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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17 except IndexError:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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18 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
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19 else:
f95f403841ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
iuc
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20 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
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21 o.writelines(sanitized_data)