Mercurial > repos > drosofff > yet_another_clipper
changeset 0:35fbec9e4bda draft
Uploaded
author | drosofff |
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date | Sat, 17 May 2014 18:12:45 -0400 |
parents | |
children | badc26214aad |
files | yac.py |
diffstat | 1 files changed, 78 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/yac.py Sat May 17 18:12:45 2014 -0400 @@ -0,0 +1,78 @@ +#!/usr/bin/python +# yac = yet another clipper +# v 0.9.1 +# Usage yac.py $input $output $adapter_to_clip $min $max $Nmode +# Christophe Antoniewski <drosofff@gmail.com> + +import sys, string + +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=""): + 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): + 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): + 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 == "accepted": + instanceClip.clip_with_N() + else: + instanceClip.clip_without_N() + +if __name__ == "__main__" : + input = sys.argv[1] + output = sys.argv[2] + adapter = sys.argv[3] + minsize = sys.argv[4] + maxsize = sys.argv[5] + Nmode = sys.argv[6] + __main__(input, output, adapter, minsize, maxsize, Nmode)