diff blastxmlToGff3.py @ 48:6803152ea92a draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 073c8ceda5eddfb4ccd07cfa96a8353e5535ffaf-dirty

--- a/blastxmlToGff3.py	Wed Mar 22 15:20:56 2017 -0400
+++ b/blastxmlToGff3.py	Tue Mar 28 18:13:27 2017 -0400
@@ -137,12 +137,18 @@
             group['parent_field']['end'] = coords[1]
             group['parent_field']['score'] = group['parent_field']['strand'] = group['parent_field']['phase'] = '.'
             group['parent_attribute']['match_num'] = match_num
+            group['alignments'].sort(key=lambda x: (x['field']['start'], x['field']['end']))
             utils.write_features(group['parent_field'], group['parent_attribute'], gff3)
+            prev_end = -1
             for align in group['alignments']:
+                overlap = ''
+                if align['field']['start'] <= prev_end:
+                    overlap += str(align['field']['start']) + ',' + str(prev_end)
+                prev_end = align['field']['end']
+                align['attribute']['overlap'] = overlap
                 utils.write_features(align['field'], align['attribute'], gff3)
     gff3.close()
 
-
 def blastxml2gff3(xml_file, gff3_file):
     result_handle = open(xml_file)
     blast_records = NCBIXML.parse(result_handle)