| Previous changeset 18:54781a26d8f3 (2017-02-01) Next changeset 20:a7de1d3c3148 (2017-04-21) |
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Commit message:
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename commit 7a746d55f0e8456992ee11c49a507285f9f39383-dirty |
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modified:
tools/seq_rename/seq_rename.py |
| b |
| diff -r 54781a26d8f3 -r 412e708d0172 tools/seq_rename/seq_rename.py --- a/tools/seq_rename/seq_rename.py Wed Feb 01 11:08:41 2017 -0500 +++ b/tools/seq_rename/seq_rename.py Fri Feb 03 12:55:57 2017 -0500 |
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| @@ -31,7 +31,9 @@ try: tabular_file, old_col_arg, new_col_arg, in_file, seq_format, out_file = sys.argv[1:] except ValueError: - sys.exit("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv))) + sys.exit("Expected six arguments (tabular file, old col, new col, " + "input file, format, output file), got %i:\n%s" + % (len(sys.argv) - 1, " ".join(sys.argv))) try: if old_col_arg.startswith("c"): @@ -128,8 +130,7 @@ in_handle.close() else: # Use Galaxy for FASTA, QUAL or FASTQ - if seq_format.lower() in ["fasta", "csfasta"] \ - or seq_format.lower().startswith("qual"): + if seq_format.lower() in ["fasta", "csfasta"] or seq_format.lower().startswith("qual"): from galaxy_utils.sequence.fasta import fastaReader, fastaWriter reader = fastaReader(open(in_file, "rU")) writer = fastaWriter(open(out_file, "w")) |