diff blastxml_to_gapped_gff3.py @ 17:4c201a3d4755 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66

--- a/blastxml_to_gapped_gff3.py	Thu Jan 25 07:58:28 2024 +0000
+++ b/blastxml_to_gapped_gff3.py	Sun Jan 28 06:48:52 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:]
@@ -290,7 +290,9 @@
         help="Trim blast hits to be only as long as the parent feature",
     )
     parser.add_argument(
-        "--trim_end", action="store_true", help="Cut blast results off at end of gene"
+        "--trim_end",
+        action="store_true",
+        help="Cut blast results off at end of gene",
     )
     parser.add_argument("--include_seq", action="store_true", help="Include sequence")
     args = parser.parse_args()