diff gff3_cleaner.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/gff3_cleaner.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+import sys
+import argparse
+from gff3 import feature_lambda, feature_test_type
+from BCBio import GFF
+import logging
+logging.basicConfig(level=logging.WARN)
+log = logging.getLogger(name='pav')
+
+def coding_genes(feature_list):
+    for x in feature_lambda(feature_list, feature_test_type, {'type': 'gene'}, subfeatures=True):
+        if len(list(feature_lambda(x.sub_features, feature_test_type, {'type': 'CDS'}, subfeatures=False))) > 0:
+            yield x
+
+
+def genes(feature_list, feature_type='gene'):
+    for x in feature_lambda(feature_list, feature_test_type,
+                            {'type': feature_type},
+                            subfeatures=True):
+        yield x
+
+
+def fix_apollo_issues(annotations, user_email):
+    for rec in GFF.parse(annotations):
+        for feat in rec.features:
+            if feat.type != 'gene':
+                continue
+
+            for sf in feat.sub_features:
+                if sf.type != 'mRNA':
+                    continue
+
+                for ssf in sf.sub_features:
+                    if ssf.type != 'exon':
+                        continue
+
+                    if len(ssf) > 10:
+                        continue
+
+                    ssf.type = 'Shine_Dalgarno_sequence'
+
+                sf.sub_features = [x for x in sf.sub_features if x.type not in
+                                   ('non_canonical_five_prime_splice_site',
+                                    'non_canonical_three_prime_splice_site')]
+        yield rec
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='rebase gff3 features against parent locations', epilog="")
+    parser.add_argument('annotations', type=file, help='Parent GFF3 annotations')
+    # parser.add_argument('genome', type=file, help='Genome Sequence')
+    parser.add_argument('--user_email')
+
+    args = parser.parse_args()
+    for rec in fix_apollo_issues(**vars(args)):
+        rec.annotations = {}
+        GFF.write([rec], sys.stdout)