Mercurial > repos > bgruening > antismash
comparison src/genecluster_sequence/__init__.py @ 22:225d40beff1a draft
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| author | bgruening |
|---|---|
| date | Mon, 14 Oct 2013 03:26:11 -0400 |
| parents | |
| children |
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| 21:93b2baa4b9d6 | 22:225d40beff1a |
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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 from os import path | |
| 8 from antismash import utils | |
| 9 | |
| 10 name = "genecluster_proteins" | |
| 11 short_description = "Ouptut gene clusters as FASTA sequences" | |
| 12 # Output plugins are sorted by priority, lower numbers get run first | |
| 13 priority = 9 | |
| 14 | |
| 15 def write(seq_records, options): | |
| 16 """Write all cluster proteins to a file | |
| 17 | |
| 18 Args: | |
| 19 seq_records (iterable): An iterable containing Bio.SeqRecords | |
| 20 options (argparse.Namespace): The options passed to the program | |
| 21 """ | |
| 22 basename = seq_records[0].id | |
| 23 output_name = path.join(options.outputfoldername, "%s_genecluster_proteins.fa" % basename) | |
| 24 logging.debug("Writing seq_records to %r" % output_name) | |
| 25 | |
| 26 with open(output_name, 'w+') as handle: | |
| 27 for seq_record in seq_records: | |
| 28 clusters = utils.get_cluster_features(seq_record) | |
| 29 for cluster in clusters: | |
| 30 clustertype = utils.get_cluster_type(cluster) | |
| 31 clusternr = utils.get_cluster_number(cluster) | |
| 32 for feature in utils.get_cluster_cds_features(cluster, seq_record): | |
| 33 qual = feature.qualifiers | |
| 34 fasta_header = '>%s:%s %s #%s - %s\n' % (qual['locus_tag'][0], qual['protein_id'][0], clustertype, clusternr, qual['product'][0]) | |
| 35 handle.write( fasta_header ) | |
| 36 handle.write( '%s\n' % qual['translation'][0] ) | |
| 37 | |
| 38 |