Mercurial > repos > bgruening > antismash
comparison src/genecluster_sequence/__init__.py @ 25:99435bb90725 draft
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| author | bgruening |
|---|---|
| date | Fri, 18 Oct 2013 03:35:17 -0400 |
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| children |
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| 24:b942dfd80819 | 25:99435bb90725 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 antiSMASH 2.0 output plugin to write all cluster proteins to a file (*_genecluster_proteins.fa) | |
| 5 """ | |
| 6 import logging | |
| 7 import textwrap | |
| 8 from os import path | |
| 9 from antismash import utils | |
| 10 | |
| 11 name = "genecluster_proteins" | |
| 12 short_description = "Ouptut gene clusters as FASTA sequences" | |
| 13 # Output plugins are sorted by priority, lower numbers get run first | |
| 14 priority = 9 | |
| 15 | |
| 16 def write(seq_records, options): | |
| 17 """Write all cluster proteins to a file | |
| 18 | |
| 19 Args: | |
| 20 seq_records (iterable): An iterable containing Bio.SeqRecords | |
| 21 options (argparse.Namespace): The options passed to the program | |
| 22 """ | |
| 23 basename = seq_records[0].id | |
| 24 output_name = path.join(options.outputfoldername, "%s_genecluster_proteins.fa" % basename) | |
| 25 logging.debug("Writing seq_records to %r" % output_name) | |
| 26 | |
| 27 with open(output_name, 'w+') as handle: | |
| 28 for seq_record in seq_records: | |
| 29 clusters = utils.get_cluster_features(seq_record) | |
| 30 for cluster in clusters: | |
| 31 clustertype = utils.get_cluster_type(cluster) | |
| 32 clusternr = utils.get_cluster_number(cluster) | |
| 33 for feature in utils.get_cluster_cds_features(cluster, seq_record): | |
| 34 qual = feature.qualifiers | |
| 35 fasta_header = '>%s:%s %s #%s - %s\n' % (qual['locus_tag'][0], qual['protein_id'][0], clustertype, clusternr, qual['product'][0]) | |
| 36 handle.write( fasta_header ) | |
| 37 handle.write( '%s\n' % '\n'.join( textwrap.wrap(qual['translation'][0], 60) ) ) |