Update polya_umi.py to include a range for seq_nano

cribbslab · Aug 11, 2023 · 96bfc19 · 96bfc19
1 parent 8d28760
commit 96bfc19
Showing 1 changed file with 5 additions and 11 deletions.
diff --git a/tallytrin/python/polya_umi.py b/tallytrin/python/polya_umi.py
@@ -107,15 +107,14 @@ def remove_indels(x, umi, first):
 
     for record in fh:
         n += 1
-        seq_nano = record.sequence
+        seq_nano = record.sequence[-200:]
 
-        m=regex.finditer("(GTACTCTGCGTTGATACCACTGCTT){e<=0}", str(record.sequence))
+        m=regex.finditer("(GTACTCTGCGTTGATACCACTGCTT){e<=0}", seq_nano)
 
+
         for i in m:
-            after_polya = seq_nano[i.start()-30:]
-            umi_polya = seq_nano[i.start()-30:i.start()]
 
-            new_umi = []
+            umi_polya = seq_nano[i.start()-30:i.start()]
 
             umi_polya, errors = remove_point_mutations(umi_polya)
 
@@ -124,16 +123,11 @@ def remove_indels(x, umi, first):
             else:
 
 
-                after_umi = seq_nano[:i.start()-30]
-
                 record_new = record.name + "_" + str(umi_polya)
 
-                quality_afterumipolya = record.quality[:i.start()-30]
-                seq_afterumipolya = seq_nano[:i.start()-30]
-
                 if len(umi_polya) == 30:
                     y += 1
-                    outfile.write("@%s\n%s\n+\n%s\n" % (record_new, seq_afterumipolya, quality_afterumipolya))
+                    outfile.write("@%s\n%s\n+\n%s\n" % (record_new, record.sequence, record.quality))
                 else:
                     pass