--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/genecluster_sequence/__init__.py	Fri Oct 18 03:35:17 2013 -0400
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+"""
+    antiSMASH 2.0 output plugin to write all cluster proteins to a file (*_genecluster_proteins.fa)
+"""
+import logging
+import textwrap
+from os import path
+from antismash import utils
+
+name = "genecluster_proteins"
+short_description = "Ouptut gene clusters as FASTA sequences"
+# Output plugins are sorted by priority, lower numbers get run first
+priority = 9
+
+def write(seq_records, options):
+    """Write all cluster proteins to a file
+
+    Args:
+        seq_records (iterable): An iterable containing Bio.SeqRecords
+        options (argparse.Namespace): The options passed to the program
+    """
+    basename = seq_records[0].id
+    output_name = path.join(options.outputfoldername, "%s_genecluster_proteins.fa" % basename)
+    logging.debug("Writing seq_records to %r" % output_name)
+
+    with open(output_name, 'w+') as handle:
+        for seq_record in seq_records:
+            clusters = utils.get_cluster_features(seq_record)
+            for cluster in clusters:
+                clustertype = utils.get_cluster_type(cluster)
+                clusternr = utils.get_cluster_number(cluster)
+                for feature in utils.get_cluster_cds_features(cluster, seq_record):
+                    qual = feature.qualifiers
+                    fasta_header = '>%s:%s %s #%s - %s\n' % (qual['locus_tag'][0], qual['protein_id'][0], clustertype, clusternr, qual['product'][0])
+                    handle.write( fasta_header )
+                    handle.write( '%s\n' % '\n'.join( textwrap.wrap(qual['translation'][0], 60) ) )