def main():
    parser = argparse.ArgumentParser(
        description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument('input', help="Use BAM or - for SAM STDIN")
    parser.add_argument('-o', '--output', help="output file")
    args = parser.parse_args()

    of = sys.stdout
    if args.output:
        if re.search('\.gz$', args.output):
            of = gzip.open(args.output, 'w')
        else:
            of = open(args.output, 'w')

    inf = sys.stdin
    if args.input != '-':
        cmd = "samtools view " + args.input
        p = Popen(cmd.split(), stdout=PIPE)
        inf = p.stdout
    for line in inf:
        v = SAM(line)
        for rng in [x.get_range() for x in v.get_target_transcript(68).exons]:
            of.write("\t".join([str(x) for x in rng.get_bed_array()]) + "\n")

    if args.input != '-':
        p.communicate()

    of.close()
Пример #2
0
def main():
  parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  parser.add_argument('input',help="Use BAM or - for SAM STDIN")
  parser.add_argument('-o','--output',help="output file")
  args = parser.parse_args()
  
  of = sys.stdout
  if args.output:
    if re.search('\.gz$',args.output):
      of = gzip.open(args.output,'w')
    else:
      of = open(args.output,'w')

  inf = sys.stdin
  if args.input != '-':
    cmd = "samtools view "+args.input
    p = Popen(cmd.split(),stdout=PIPE)
    inf = p.stdout
  for line in inf:
    v = SAM(line)
    for rng in [x.get_range() for x in v.get_target_transcript(68).exons]:
      of.write("\t".join([str(x) for x in rng.get_bed_array()])+"\n")

  if args.input != '-':
    p.communicate()    

  of.close()
 def get_SAM(self, min_intron_size=68):
     from Bio.Format.Sam import SAM
     #ar is target then query
     qname = self.get_alignment_ranges()[0][1].chr
     flag = 0
     if self.get_strand() == '-': flag = 16
     rname = self.get_alignment_ranges()[0][0].chr
     pos = self.get_alignment_ranges()[0][0].start
     mapq = 255
     cigar = self.construct_cigar(min_intron_size)
     rnext = '*'
     pnext = 0
     tlen = self.get_target_range().length()
     seq = self.get_query_sequence()
     if not seq: seq = '*'
     qual = self.get_query_quality()
     if not qual: qual = '*'
     #seq = '*'
     #qual = '*'
     if self.get_strand() == '-':
         seq = rc(seq)
         qual = qual[::-1]
     ln = qname + "\t" + str(flag) + "\t" + rname + "\t" + \
          str(pos) + "\t" + str(mapq) + "\t" + cigar + "\t" + \
          rnext + "\t" + str(pnext) + "\t" + str(tlen) + "\t" + \
          seq + "\t" + qual
     return SAM(ln, reference=self._reference)
def do_seq(seq,args,fname):
  cmd = 'samtools view '+args.input+' '+seq
  p = Popen(cmd.split(),stdout=PIPE)
  cmd = 'bedtools genomecov -i - -bg -g '+fname
  po2 = Popen(cmd.split(),stdin=PIPE,stdout=PIPE)
  cmd = 'sort -k 1,1 -k2,2n -k3,3n -S1G --parallel='+str(args.threads)
  if args.tempdir: cmd += ' -T '+args.tempdir
  po1 = Popen(cmd.split(),stdin=PIPE,stdout=po2.stdin)
  for line in p.stdout:
    sam = SAM(line)
    if not sam.is_aligned(): continue
    for ex in sam.get_target_transcript(min_intron=68).exons:
      bed = "\t".join([str(x) for x in ex.get_range().get_bed_array()])
      po1.stdin.write(bed+"\n")
  po1.communicate()
  res = po2.communicate()[0]
  return res
def do_seq(seq, args, fname):
    cmd = 'samtools view ' + args.input + ' ' + seq
    p = Popen(cmd.split(), stdout=PIPE)
    cmd = 'bedtools genomecov -i - -bg -g ' + fname
    po2 = Popen(cmd.split(), stdin=PIPE, stdout=PIPE)
    cmd = 'sort -k 1,1 -k2,2n -k3,3n -S1G --parallel=' + str(args.threads)
    if args.tempdir: cmd += ' -T ' + args.tempdir
    po1 = Popen(cmd.split(), stdin=PIPE, stdout=po2.stdin)
    for line in p.stdout:
        sam = SAM(line)
        if not sam.is_aligned(): continue
        for ex in sam.get_target_transcript(min_intron=68).exons:
            bed = "\t".join([str(x) for x in ex.get_range().get_bed_array()])
            po1.stdin.write(bed + "\n")
    po1.communicate()
    res = po2.communicate()[0]
    return res