Merge pull request #7 from PennChopMicrobiomeProgram/VT_edit

Moved coordinate change to matcher.py
PennChopMicrobiomeProgram · Jun 23, 2021 · be037e7 · be037e7
2 parents dab46e1 + c07cfed
commit be037e7
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/primertrim/align.py b/primertrim/align.py
@@ -111,8 +111,4 @@ def parse(self, f):
                 for field in self.fields:
                     fcn = BLAST_FIELD_TYPES[field]
                     res[field] = fcn(res[field])
-            if res["qstrand"] == "-":
-                qstart_temp = res["qlen"]-res["qend"]+1
-                res["qend"] = res["qlen"]-res["qstart"]+1
-                res["qstart"] = qstart_temp
             yield res
diff --git a/primertrim/matcher.py b/primertrim/matcher.py
@@ -141,6 +141,9 @@ def find_in_seqs(self, seqs):
             # Vsearch indexes positions starting with 1
             start_idx = hit["qstart"] - 1
             end_idx = hit["qend"]
+            if hit["qstrand"] == "-":
+                start_idx = hit["qlen"]-hit["qend"]
+                end_idx = hit["qlen"]-hit["qstart"]+1
             assert(start_idx < end_idx)
             seq = seqs[seq_id]
             primerseq = seq[start_idx:end_idx]