included adapter checks

MicrobiologyETHZ · Sep 22, 2023 · e94d23f · e94d23f
1 parent 4f443a6
commit e94d23f
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/wish_tags_generator.py b/wish_tags_generator.py
@@ -75,7 +75,9 @@ def check_tm(seq):
 def check_palindrome(seq):
     return(fast_rc(seq)!=seq)
 
-def check_hairpins(seq):
+def check_hairpins(seq, adapter=None):
+    if adapter is not None:
+        seq = adapter+seq
     trimers = []
     rc_trimers = []
     for offset in range(0,3):
@@ -163,6 +165,8 @@ def gen_primers(l,n,pool):
     seqs = filter(check_palindrome, seqs)
     seqs = filter(check_runs, seqs)
     seqs = filter(check_hairpins, seqs)
+    seqs = filter(lambda x: check_hairpins(x, 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'))
+    seqs = filter(lambda x: check_hairpins(x, 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'))
     seqs = list(dict.fromkeys(seqs))
     sys.stdout.write("{} of {} random {}mers passed initial checks.\n".format(len(seqs), n, l))
     aln = run_bwa(seqs)