diff jbrowse2/blastxml_to_gapped_gff3.py @ 7:234cf4490901 draft

Uploaded
author fubar
date Fri, 05 Jan 2024 04:31:35 +0000
parents 88b9b105c09b
children
line wrap: on
line diff
--- a/jbrowse2/blastxml_to_gapped_gff3.py	Fri Jan 05 01:58:02 2024 +0000
+++ b/jbrowse2/blastxml_to_gapped_gff3.py	Fri Jan 05 04:31:35 2024 +0000
@@ -32,7 +32,7 @@
 
         recid = record.query
         if " " in recid:
-            recid = recid[0 : recid.index(" ")]
+            recid = recid[0: recid.index(" ")]
 
         rec = SeqRecord(Seq("ACTG"), id=recid)
         for idx_hit, hit in enumerate(record.alignments):
@@ -72,7 +72,7 @@
                     qualifiers["blast_" + prop] = getattr(hsp, prop, None)
 
                 desc = hit.title.split(" >")[0]
-                qualifiers["description"] = desc[desc.index(" ") :]
+                qualifiers["description"] = desc[desc.index(" "):]
 
                 # This required a fair bit of sketching out/match to figure out
                 # the first time.
@@ -161,9 +161,9 @@
     fm = ""
     fs = ""
     for position in re.finditer("-", query):
-        fq += query[prev : position.start()]
-        fm += match[prev : position.start()]
-        fs += subject[prev : position.start()]
+        fq += query[prev: position.start()]
+        fm += match[prev: position.start()]
+        fs += subject[prev: position.start()]
         prev = position.start() + 1
     fq += query[prev:]
     fm += match[prev:]