--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/yac.py	Mon Nov 03 09:34:45 2014 -0500
@@ -0,0 +1,91 @@
+#!/usr/bin/python
+# yac = yet another clipper
+# v 1.1.0 - 23-08-2014 - argparse implementation
+# Usage yac.py  $input $output $adapter_to_clip $min $max $Nmode
+# Christophe Antoniewski <drosofff@gmail.com>
+
+import sys, string, argparse
+
+def Parser():
+  the_parser = argparse.ArgumentParser()
+  the_parser.add_argument('--input', action="store", type=str, help="input fastq file")
+  the_parser.add_argument('--output', action="store", type=str, help="output, clipped fasta file")
+  the_parser.add_argument('--adapter_to_clip', action="store", type=str, help="adapter sequence to clip")
+  the_parser.add_argument('--min', action="store", type=int, help="minimal size of clipped sequence to keep")
+  the_parser.add_argument('--max', action="store", type=int, help="maximal size of clipped sequence to keep")
+  the_parser.add_argument('--Nmode', action="store", type=str, choices=["accept", "reject"], help="accept or reject sequences with N for clipping")
+  args = the_parser.parse_args()
+  args.adapter_to_clip = args.adapter_to_clip.upper()
+  return args
+
+
+class Clip:
+  def __init__(self, inputfile, outputfile, adapter, minsize, maxsize):
+    self.inputfile = inputfile
+    self.outputfile = outputfile
+    self.adapter = adapter
+    self.minsize = int(minsize)
+    self.maxsize = int(maxsize)
+    def motives (sequence):
+      '''return a list of motives for perfect (6nt) or imperfect (7nt with one mismatch) search on import string module'''
+      sequencevariants = [sequence[0:6]] # initializes the list with the 6mer perfect match
+      dicsubst= {"A":"TGCN", "T":"AGCN", "G":"TACN", "C":"GATN"}
+      for pos in enumerate(sequence[:6]):
+        for subst in dicsubst[pos[1]]:
+          sequencevariants.append(sequence[:pos[0]]+ subst + sequence[pos[0]+1:7])
+      return sequencevariants
+    self.adaptmotifs= motives(self.adapter)
+
+  def scanadapt(self, adaptmotives=[], sequence=""):
+    '''scans sequence for adapter motives'''
+    if sequence.rfind(adaptmotives[0]) != -1:
+      return sequence[:sequence.rfind(adaptmotives[0])]
+    for motif in adaptmotives[1:]:
+      if sequence.rfind(motif) != -1:
+        return sequence[:sequence.rfind(motif)]
+    return sequence
+
+  def clip_with_N (self):
+    '''clips adapter sequences from inputfile. 
+    Reads containing N are retained.'''
+    iterator = 0
+    id = 0
+    F = open (self.inputfile, "r")
+    O = open (self.outputfile, "w")
+    for line in F:
+      iterator += 1
+      if iterator % 4 == 2:
+        trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
+        if self.minsize <= len(trim) <= self.maxsize:
+          id += 1
+          print >> O, ">%i\n%s" % (id, trim)
+    F.close()
+    O.close()
+  def clip_without_N (self):
+    '''clips adapter sequences from inputfile. 
+    Reads containing N are rejected.'''
+    iterator = 0
+    id = 0
+    F = open (self.inputfile, "r")
+    O = open (self.outputfile, "w")
+    for line in F:
+      iterator += 1
+      if iterator % 4 == 2:
+        trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
+        if "N" in trim: continue
+        if self.minsize <= len(trim) <= self.maxsize:
+          id += 1
+          print >> O, ">%i\n%s" % (id, trim)
+    F.close()
+    O.close()
+
+def __main__ (inputfile, outputfile, adapter, minsize, maxsize, Nmode):
+  instanceClip = Clip (inputfile, outputfile, adapter, minsize, maxsize)
+  if Nmode == "accept":
+    instanceClip.clip_with_N()
+  else:
+    instanceClip.clip_without_N()
+
+if __name__ == "__main__" :
+  args = Parser()
+  __main__(args.input, args.output, args.adapter_to_clip, args.min, args.max, args.Nmode)