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1 #!/usr/bin/python
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2 # yac = yet another clipper
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3 # v 1.0.0
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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
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8
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9 class Clip:
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10 def __init__(self, inputfile, outputfile, adapter, minsize, maxsize):
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11 self.inputfile = inputfile
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12 self.outputfile = outputfile
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13 self.adapter = adapter
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14 self.minsize = int(minsize)
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15 self.maxsize = int(maxsize)
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16 def motives (sequence):
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17 '''return a list of motives for perfect (6nt) or imperfect (7nt with one mismatch) search on import string module'''
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18 sequencevariants = [sequence[0:6]] # initializes the list with the 6mer perfect match
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19 dicsubst= {"A":"TGCN", "T":"AGCN", "G":"TACN", "C":"GATN"}
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20 for pos in enumerate(sequence[:6]):
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21 for subst in dicsubst[pos[1]]:
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22 sequencevariants.append(sequence[:pos[0]]+ subst + sequence[pos[0]+1:7])
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23 return sequencevariants
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24 self.adaptmotifs= motives(self.adapter)
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25
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26 def scanadapt(self, adaptmotives=[], sequence=""):
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27 '''scans sequence for adapter motives'''
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28 if sequence.rfind(adaptmotives[0]) != -1:
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29 return sequence[:sequence.rfind(adaptmotives[0])]
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30 for motif in adaptmotives[1:]:
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31 if sequence.rfind(motif) != -1:
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32 return sequence[:sequence.rfind(motif)]
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33 return sequence
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34
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35 def clip_with_N (self):
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36 '''clips adapter sequences from inputfile.
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37 Reads containing N are retained.'''
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38 iterator = 0
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39 id = 0
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40 F = open (self.inputfile, "r")
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41 O = open (self.outputfile, "w")
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42 for line in F:
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43 iterator += 1
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44 if iterator % 4 == 2:
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45 trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
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46 if self.minsize <= len(trim) <= self.maxsize:
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47 id += 1
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48 print >> O, ">%i\n%s" % (id, trim)
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49 F.close()
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50 O.close()
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51 def clip_without_N (self):
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52 '''clips adapter sequences from inputfile.
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53 Reads containing N are rejected.'''
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54 iterator = 0
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55 id = 0
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56 F = open (self.inputfile, "r")
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57 O = open (self.outputfile, "w")
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58 for line in F:
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59 iterator += 1
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60 if iterator % 4 == 2:
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61 trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
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62 if "N" in trim: continue
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63 if self.minsize <= len(trim) <= self.maxsize:
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64 id += 1
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65 print >> O, ">%i\n%s" % (id, trim)
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66 F.close()
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67 O.close()
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68
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69 def __main__ (inputfile, outputfile, adapter, minsize, maxsize, Nmode):
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70 instanceClip = Clip (inputfile, outputfile, adapter, minsize, maxsize)
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71 if Nmode == "accept":
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72 instanceClip.clip_with_N()
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73 else:
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74 instanceClip.clip_without_N()
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75
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76 if __name__ == "__main__" :
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77 input = sys.argv[1]
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78 output = sys.argv[2]
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79 adapter = sys.argv[3]
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80 minsize = sys.argv[4]
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81 maxsize = sys.argv[5]
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82 Nmode = sys.argv[6]
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83 __main__(input, output, adapter, minsize, maxsize, Nmode)
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