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1 #!/usr/bin/python
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2 # yac = yet another clipper
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3 # v 1.1.0 - 23-08-2014 - argparse implementation
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4 # Usage yac.py $input $output $adapter_to_clip $min $max $Nmode
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5 # Christophe Antoniewski <drosofff@gmail.com>
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6
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7 import sys, string, argparse
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8
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9 def Parser():
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10 the_parser = argparse.ArgumentParser()
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11 the_parser.add_argument('--input', action="store", type=str, help="input fastq file")
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12 the_parser.add_argument('--output', action="store", type=str, help="output, clipped fasta file")
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13 the_parser.add_argument('--adapter_to_clip', action="store", type=str, help="adapter sequence to clip")
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14 the_parser.add_argument('--min', action="store", type=int, help="minimal size of clipped sequence to keep")
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15 the_parser.add_argument('--max', action="store", type=int, help="maximal size of clipped sequence to keep")
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16 the_parser.add_argument('--Nmode', action="store", type=str, choices=["accept", "reject"], help="accept or reject sequences with N for clipping")
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17 args = the_parser.parse_args()
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18 args.adapter_to_clip = args.adapter_to_clip.upper()
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19 return args
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20
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21
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22 class Clip:
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23 def __init__(self, inputfile, outputfile, adapter, minsize, maxsize):
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24 self.inputfile = inputfile
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25 self.outputfile = outputfile
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26 self.adapter = adapter
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27 self.minsize = int(minsize)
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28 self.maxsize = int(maxsize)
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29 def motives (sequence):
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30 '''return a list of motives for perfect (6nt) or imperfect (7nt with one mismatch) search on import string module'''
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31 sequencevariants = [sequence[0:6]] # initializes the list with the 6mer perfect match
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32 dicsubst= {"A":"TGCN", "T":"AGCN", "G":"TACN", "C":"GATN"}
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33 for pos in enumerate(sequence[:6]):
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34 for subst in dicsubst[pos[1]]:
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35 sequencevariants.append(sequence[:pos[0]]+ subst + sequence[pos[0]+1:7])
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36 return sequencevariants
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37 self.adaptmotifs= motives(self.adapter)
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38
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39 def scanadapt(self, adaptmotives=[], sequence=""):
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40 '''scans sequence for adapter motives'''
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41 if sequence.rfind(adaptmotives[0]) != -1:
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42 return sequence[:sequence.rfind(adaptmotives[0])]
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43 for motif in adaptmotives[1:]:
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44 if sequence.rfind(motif) != -1:
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45 return sequence[:sequence.rfind(motif)]
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46 return sequence
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47
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48 def clip_with_N (self):
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49 '''clips adapter sequences from inputfile.
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50 Reads containing N are retained.'''
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51 iterator = 0
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52 id = 0
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53 F = open (self.inputfile, "r")
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54 O = open (self.outputfile, "w")
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55 for line in F:
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56 iterator += 1
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57 if iterator % 4 == 2:
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58 trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
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59 if self.minsize <= len(trim) <= self.maxsize:
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60 id += 1
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61 print >> O, ">%i\n%s" % (id, trim)
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62 F.close()
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63 O.close()
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64 def clip_without_N (self):
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65 '''clips adapter sequences from inputfile.
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66 Reads containing N are rejected.'''
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67 iterator = 0
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68 id = 0
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69 F = open (self.inputfile, "r")
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70 O = open (self.outputfile, "w")
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71 for line in F:
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72 iterator += 1
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73 if iterator % 4 == 2:
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74 trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
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75 if "N" in trim: continue
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76 if self.minsize <= len(trim) <= self.maxsize:
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77 id += 1
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78 print >> O, ">%i\n%s" % (id, trim)
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79 F.close()
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80 O.close()
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81
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82 def __main__ (inputfile, outputfile, adapter, minsize, maxsize, Nmode):
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83 instanceClip = Clip (inputfile, outputfile, adapter, minsize, maxsize)
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84 if Nmode == "accept":
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85 instanceClip.clip_with_N()
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86 else:
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87 instanceClip.clip_without_N()
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88
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89 if __name__ == "__main__" :
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90 args = Parser()
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91 __main__(args.input, args.output, args.adapter_to_clip, args.min, args.max, args.Nmode)
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