comparison yac.py @ 0:35fbec9e4bda draft

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author drosofff
date Sat, 17 May 2014 18:12:45 -0400
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-1:000000000000 0:35fbec9e4bda
1 #!/usr/bin/python
2 # yac = yet another clipper
3 # v 0.9.1
4 # Usage yac.py $input $output $adapter_to_clip $min $max $Nmode
5 # Christophe Antoniewski <drosofff@gmail.com>
6
7 import sys, string
8
9 class Clip:
10 def __init__(self, inputfile, outputfile, adapter, minsize, maxsize):
11 self.inputfile = inputfile
12 self.outputfile = outputfile
13 self.adapter = adapter
14 self.minsize = int(minsize)
15 self.maxsize = int(maxsize)
16 def motives (sequence):
17 '''return a list of motives for perfect (6nt) or imperfect (7nt with one mismatch) search on import string module'''
18 sequencevariants = [sequence[0:6]] # initializes the list with the 6mer perfect match
19 dicsubst= {"A":"TGCN", "T":"AGCN", "G":"TACN", "C":"GATN"}
20 for pos in enumerate(sequence[:6]):
21 for subst in dicsubst[pos[1]]:
22 sequencevariants.append(sequence[:pos[0]]+ subst + sequence[pos[0]+1:7])
23 return sequencevariants
24 self.adaptmotifs= motives(self.adapter)
25
26 def scanadapt(self, adaptmotives=[], sequence=""):
27 if sequence.rfind(adaptmotives[0]) != -1:
28 return sequence[:sequence.rfind(adaptmotives[0])]
29 for motif in adaptmotives[1:]:
30 if sequence.rfind(motif) != -1:
31 return sequence[:sequence.rfind(motif)]
32 return sequence
33
34 def clip_with_N (self):
35 iterator = 0
36 id = 0
37 F = open (self.inputfile, "r")
38 O = open (self.outputfile, "w")
39 for line in F:
40 iterator += 1
41 if iterator % 4 == 2:
42 trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
43 if self.minsize <= len(trim) <= self.maxsize:
44 id += 1
45 print >> O, ">%i\n%s" % (id, trim)
46 F.close()
47 O.close()
48 def clip_without_N (self):
49 iterator = 0
50 id = 0
51 F = open (self.inputfile, "r")
52 O = open (self.outputfile, "w")
53 for line in F:
54 iterator += 1
55 if iterator % 4 == 2:
56 trim = self.scanadapt (self.adaptmotifs, line.rstrip() )
57 if "N" in trim: continue
58 if self.minsize <= len(trim) <= self.maxsize:
59 id += 1
60 print >> O, ">%i\n%s" % (id, trim)
61 F.close()
62 O.close()
63
64 def __main__ (inputfile, outputfile, adapter, minsize, maxsize, Nmode):
65 instanceClip = Clip (inputfile, outputfile, adapter, minsize, maxsize)
66 if Nmode == "accepted":
67 instanceClip.clip_with_N()
68 else:
69 instanceClip.clip_without_N()
70
71 if __name__ == "__main__" :
72 input = sys.argv[1]
73 output = sys.argv[2]
74 adapter = sys.argv[3]
75 minsize = sys.argv[4]
76 maxsize = sys.argv[5]
77 Nmode = sys.argv[6]
78 __main__(input, output, adapter, minsize, maxsize, Nmode)