was CG9.py. limits seq repeats from fastq files. arg1=trunc to number…

…, arg2=repeated string, arg3=filename.

trunc_rep.py

@@ -0,0 +1,25 @@
+#! /usr/bin/env python
+import sys, screed, re
+
+# "rep" = "repeat"
+
+rep_num = int(sys.argv[1])
+rep_str = sys.argv[2]
+
+trunc_rep = rep_str * rep_num
+
+rep_pat_txt = trunc_rep + rep_str + '+'
+rep_pat = re.compile (rep_pat_txt)
+
+for record in screed.open(sys.argv[3]):
+   name = record.name
+   sequence = record.sequence
+   qual = record.accuracy
+
+   for match in rep_pat.finditer(sequence):
+      qual_chop_end = match.start() + rep_num * len(rep_str)
+      qual = qual[0:qual_chop_end] + qual[match.end():]
+
+   sequence = rep_pat.sub(trunc_rep, sequence)
+
+   print '@%s\n%s\n+\n%s' % (name, sequence, qual)