Mercurial > repos > yating-l > jbrowse_hub

diff blastxmlToGff3.py @ 31:d8049deb0c97 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 12:28:32 -0400
parents e4f3f2ed4fa5
children 15b4a74722d1
line wrap: on
line diff
--- a/blastxmlToGff3.py	Wed Mar 15 11:46:38 2017 -0400
+++ b/blastxmlToGff3.py	Fri Mar 17 12:28:32 2017 -0400
@@ -7,14 +7,14 @@
 
 
 def align2cigar(hsp_query, hsp_reference):
-    '''
+    """
         Build CIGAR representation from an hsp_query
         input:
             hsp_query
             hsp_sbjct
         output:
             CIGAR string
-    '''
+    """
     query = hsp_query
     ref = hsp_reference
     # preType, curType:
@@ -98,6 +98,8 @@
                 attribute['ID'] = field['seqid'] + '_' + str(field['start']) + '_' + str(field['end']) + '_' + query_name + '_' + str(target_start) + '_' + str(target_end)
                 attribute['Target'] = query_name + " " + str(target_start) + " " + str(target_end)
                 attribute['Gap'] = align2cigar(query, ref)
+                #store the query sequence in the file in order to display alignment with BlastAlignment plugin
+                attribute['query'] = hsp.query
                 # show reading frame attribute only if the frame is not (0, 0)
                 if hsp.frame[0] != 0 or hsp.frame[1] != 0:
                     attribute['reading_frame'] = str(hsp.frame[0]) + ", " + str(hsp.frame[1])