Mercurial > repos > devteam > tabular_to_fastq
diff tabular_to_fastq.py @ 5:e8ca9af08774 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author | iuc |
---|---|
date | Wed, 19 Feb 2020 17:08:16 +0000 |
parents | 643018aa1435 |
children |
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--- a/tabular_to_fastq.py Fri Nov 01 13:22:35 2019 -0400 +++ b/tabular_to_fastq.py Wed Feb 19 17:08:16 2020 +0000 @@ -14,15 +14,14 @@ max_col = max(identifier_col, sequence_col, quality_col) num_reads = None skipped_lines = 0 - out = open(output_filename, 'w') - for num_reads, line in enumerate(open(input_filename)): - fields = line.rstrip('\n\r').split('\t') - if len(fields) > max_col: - out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col])) - else: - skipped_lines += 1 + with open(output_filename, 'w') as out: + for num_reads, line in enumerate(open(input_filename)): + fields = line.rstrip('\n\r').split('\t') + if len(fields) > max_col: + out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col])) + else: + skipped_lines += 1 - out.close() if num_reads is None: print("Input was empty.") else: