diff export.py @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+import StringIO
+import sys
+import json
+import argparse
+from Bio import SeqIO
+from BCBio import GFF
+from webapollo import WebApolloInstance
+
+if __name__ == '__main__':
+    json
+    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
+    parser.add_argument('apollo', help='Complete Apollo URL')
+    parser.add_argument('username', help='WA Username')
+    parser.add_argument('password', help='WA Password')
+
+    parser.add_argument('commonName', nargs='+', help='Sequence Unique Names')
+
+    parser.add_argument('--gff', type=argparse.FileType('w'))
+    parser.add_argument('--fasta', type=argparse.FileType('w'))
+
+    args = parser.parse_args()
+
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+
+    data = StringIO.StringIO(wa.io.write(
+        exportType='GFF3',
+        seqType='genomic',
+        exportAllSequences=False,
+        exportGff3Fasta=True,
+        output="text",
+        exportFormat="text",
+        # TODO: CPT specific convention!!!!!!!!
+        organism=args.commonName,
+        sequences=args.commonName
+    ))
+    data.seek(0)
+
+    for record in GFF.parse(data):
+        record.annotations = {}
+        GFF.write([record], args.gff)
+        record.description = ""
+        SeqIO.write([record], args.fasta, 'fasta')
+        sys.exit()