diff export.py @ 0:cd595b5d890a draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export.py	Mon Sep 11 05:46:00 2017 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import json
+import sys
+
+from BCBio import GFF
+
+from Bio import SeqIO
+
+from future import standard_library
+
+from webapollo import CnOrGuess, GuessCn, WAAuth, WebApolloInstance
+
+standard_library.install_aliases()
+try:
+    import StringIO as io
+except ImportError:
+    import io
+
+
+def export(org_cn, seqs):
+    org_data = wa.organisms.findOrganismByCn(org_cn)
+
+    data = io.StringIO()
+
+    kwargs = dict(
+        exportType='GFF3',
+        seqType='genomic',
+        exportGff3Fasta=True,
+        output="text",
+        exportFormat="text",
+        organism=org_cn,
+    )
+
+    if len(seqs) > 0:
+        data.write(wa.io.write(
+            exportAllSequences=False,
+            sequences=seqs,
+            **kwargs
+        ).encode('utf-8'))
+    else:
+        data.write(wa.io.write(
+            exportAllSequences=True,
+            sequences=[],
+            **kwargs
+        ).encode('utf-8'))
+
+    # Seek back to start
+    data.seek(0)
+
+    records = list(GFF.parse(data))
+    if len(records) == 0:
+        print("Could not find any sequences or annotations for this organism + reference sequence")
+        sys.exit(2)
+    else:
+        for record in records:
+            record.annotations = {}
+            record.features = sorted(record.features, key=lambda x: x.location.start)
+            if args.gff:
+                GFF.write([record], args.gff)
+            record.description = ""
+            if args.fasta:
+                SeqIO.write([record], args.fasta, 'fasta')
+
+    return org_data
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
+    WAAuth(parser)
+    CnOrGuess(parser)
+    parser.add_argument('--gff', type=argparse.FileType('w'))
+    parser.add_argument('--fasta', type=argparse.FileType('w'))
+    parser.add_argument('--json', type=argparse.FileType('w'))
+
+    args = parser.parse_args()
+
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+
+    org_cn_list, seqs = GuessCn(args, wa)
+
+    org_data = []
+    for org_cn in org_cn_list:
+        indiv_org_data = export(org_cn, seqs)
+        org_data.append(indiv_org_data)
+    args.json.write(json.dumps(org_data, indent=2))