annotate mergeCols.py @ 3:ae7843d06f8f draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit ed2daf7024ea79a04bbb4a0896b9402ab2daf89f"

import sys


def __main__():
    if len(sys.argv) < 4:
        sys.exit('No columns to merge\n')
    else:
        cols = sys.argv[3:]

    with open(sys.argv[1], 'r') as infile, open(sys.argv[2], 'w') as outfile:
        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

            outfile.write("{}\n".format(line))

    if skipped_lines > 0:
        print('Skipped %d invalid lines' % skipped_lines)


if __name__ == "__main__":
    __main__()