tools/data_tools/parseGff.py

   1 #!/usr/bin/env python
   2 # -*- coding: utf-8 -*-
   3
   4 import sys
   5 import os.path
   6 import csv
   7 from PyGff import *
   8 import cPickle
   9 import copy
  10
  11 def parse(gff_fid,pickle_fid):
  12    reader = csv.reader(gff_fid, delimiter='\t', quoting=csv.QUOTE_NONE)
  13
  14    allGenes = []
  15    currentGene = None
  16
  17    for row in reader:
  18       assert len(row) == 9
  19       chr = row[0]
  20       id = row[2]
  21       start = int(row[3])
  22       stop = int(row[4])
  23       strand = row[6]
  24
  25       if id == 'chromosome':
  26          continue
  27
  28       if id == 'gene':
  29          if currentGene != None:
  30             allGenes.append(currentGene)
  31
  32          currentGene = Gene(chr,start,stop,strand)
  33
  34       elif id == 'five_prime_UTR':
  35          pass
  36
  37       elif id == 'three_prime_UTR':
  38          pass
  39
  40       elif id == 'mRNA':
  41          pass
  42
  43       elif id == 'exon':
  44          assert currentGene != None
  45          currentGene.addExon(start,stop)
  46
  47       elif id == 'CDS':
  48          pass
  49
  50       elif id == 'ncRNA':
  51          pass
  52
  53       elif id == 'pseudogenic_exon':
  54          pass
  55
  56       elif id == 'pseudogenic_transcript':
  57          pass
  58
  59       elif id == 'miRNA':
  60          pass
  61
  62       elif id == 'rRNA':
  63          pass
  64
  65       elif id == 'snoRNA':
  66          pass
  67
  68       elif id == 'snRNA':
  69          pass
  70
  71       elif id == 'tRNA':
  72          pass
  73
  74       elif id == 'pseudogene':
  75          if currentGene != None:
  76             allGenes.append(currentGene)
  77             currentGene = None
  78       else:
  79          assert False, 'Error: Unknown identifier \'%s\'' % id
  80
  81    if currentGene != None:
  82       allGenes.append(currentGene)
  83
  84    cPickle.dump(allGenes,pickle_fid)
  85
  86 if __name__ == '__main__':
  87    assert len(sys.argv) >= 3
  88    annotFile = sys.argv[1]
  89    pickleFile = sys.argv[2]
  90    assert os.path.exists(annotFile)
  91    assert not os.path.exists(pickleFile)
  92
  93    gff_fid = open(annotFile)
  94    pickle_fid = open(pickleFile,'w+')
  95    parse(gff_fid,pickle_fid)