Mercurial > repos > iuc > smgu_frameshift_deletions_checks
view frameshift_deletions_report_fixer.py @ 1:029d90b0c4f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
author | iuc |
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date | Fri, 14 Jul 2023 22:07:22 +0000 |
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"""Polish the output of the frameshift_deletions_check command. - Drops the first index column, which is rather pointless to include - Turns ref bases printed as literal bytes strings into plain output - Removes [] around pos lists and spaces after comma separating list elements - Turns None and empty list values into . as a cell placeholder """ import re import sys def matchrepl(matchobj): bytes_string_content = matchobj.group(1) if bytes_string_content is not None: return bytes_string_content list_content = matchobj.group(2) if list_content is not None: if list_content == '': return '.' return list_content.replace(', ', ',') none_cell = matchobj.group(3) if none_cell is not None: return '\t.\t' raise ValueError('Error in regex parsing code') if __name__ == '__main__': regex = re.compile(r"b'(.+)'|\[([^\]]*)\]|\t(None)\t") with open(sys.argv[1]) as i: with open(sys.argv[2], 'w') as o: for line in i: line = line[line.index('\t') + 1:] o.write(regex.sub(matchrepl, line))