tools/data_tools/parseSolexa.py

   1 #!/usr/bin/env python
   2 # -*- coding: utf-8 -*-
   3
   4 import sys
   5 import os.path
   6 import cPickle
   7 import csv
   8 from Solexa import Read
   9
  10 def parse(solexa_fid,pickle_fid):
  11
  12    reader = csv.reader(solexa_fid, delimiter='\t', quoting=csv.QUOTE_NONE)
  13
  14    allReads = []
  15    currentRead = None
  16
  17    stmap = {'P':'-','D':'+'}
  18
  19    for row in reader:
  20       assert len(row) == 12
  21       chr = row[0]
  22       pos = row[1]
  23       seq = row[2]
  24       id = int(row[3])
  25       strand = stmap[row[4]]
  26       mismatch = row[5]
  27       repeat = row[6]
  28       length = row[7]
  29       deletion = row[8]
  30
  31       prob = row[9]
  32       calibratedProb = row[10]
  33       chastity = row[11]
  34
  35       prob = [ord(elem)-50 for elem in prob]
  36       calibratedProb = [ord(elem)-64 for elem in calibratedProb]
  37       chastity = [ord(elem)+10 for elem in chastity]
  38
  39       currentRead = Read(chr,pos,seq,strand,prob,calibratedProb,chastity)
  40       allReads.append(currentRead)
  41
  42    cPickle.dump(allReads,pickle_fid)
  43
  44 if __name__ == '__main__':
  45    assert len(sys.argv) >= 3
  46    solexaFile = sys.argv[1]
  47    pickleFile = sys.argv[2]
  48    assert os.path.exists(solexaFile)
  49    assert not os.path.exists(pickleFile)
  50
  51    solexa_fid = open(solexaFile)
  52    pickle_fid = open(pickleFile,'w+')
  53    parse(solexa_fid,pickle_fid)
  54