Mercurial > repos > devteam > merge_cols
view mergeCols.py @ 2:dd40b1e9eebe draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
author | devteam |
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date | Wed, 03 Jun 2020 10:22:39 -0400 |
parents | 28ca7552e884 |
children | ae7843d06f8f |
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import sys def __main__(): try: infile = open(sys.argv[1], 'r') outfile = open(sys.argv[2], 'w') except Exception: sys.exit('Cannot open or create a file\n') if len(sys.argv) < 4: sys.exit('No columns to merge\n') else: cols = sys.argv[3:] skipped_lines = 0 for line in infile: line = line.rstrip('\r\n') if line and not line.startswith('#'): fields = line.split('\t') line += '\t' for col in cols: try: line += fields[int(col) - 1] except Exception: skipped_lines += 1 print(line, file=outfile) if skipped_lines > 0: print('Skipped %d invalid lines' % skipped_lines) if __name__ == "__main__": __main__()