コード例 #1
0
def do_quality_any(fastq, rnum):
    sequence = fastq.seq
    quality = fastq.qual
    #five possible errors 3 base changes a deletion or insertion
    seq = ''
    qual = ''
    for i in range(0, len(sequence)):
        rate = phred33_to_rate(quality[i])
        if rnum.random() > rate:
            seq += sequence[i]
            qual += quality[i]
            continue
        type = rnum.choice(['ins', 'del', 'mis', 'mis', 'mis'])
        if type == 'mis':
            seq += rnum.different_random_nt(sequence[i])
            qual += quality[i]
        elif type == 'ins':
            if rnum.random() < 0.5:
                seq += sequence[i] + rnum.random_nt()
                qual += quality[i] + quality[i]
            else:
                seq += rnum.random_nt() + sequence[i]
                qual += quality[i] + quality[i]
        #for del type we do nothing ... cause its not getting added
    return Fastq([fastq.name, seq, '+', qual])
コード例 #2
0
ファイル: emit.py プロジェクト: jason-weirather/Au-public
def do_quality_any(fastq,rnum):
  sequence = fastq.seq
  quality = fastq.qual
  #five possible errors 3 base changes a deletion or insertion
  seq = ''
  qual = ''
  for i in range(0,len(sequence)):
    rate = phred33_to_rate(quality[i])
    if rnum.random() > rate:
      seq += sequence[i]
      qual += quality[i]
      continue
    type = rnum.choice(['ins','del','mis','mis','mis'])
    if type == 'mis':
      seq += rnum.different_random_nt(sequence[i])
      qual += quality[i]
    elif type == 'ins':
      if rnum.random() < 0.5:
        seq += sequence[i]+rnum.random_nt()
        qual += quality[i]+quality[i]
      else:
        seq += rnum.random_nt()+sequence[i]
        qual += quality[i]+quality[i]
    #for del type we do nothing ... cause its not getting added
  return Fastq([fastq.name,seq,'+',qual])
コード例 #3
0
def do_quality_mismatch(fastq, rnum):
    sequence = fastq.seq
    quality = fastq.qual
    #five possible errors 3 base changes a deletion or insertion
    seq = ''
    qual = ''
    for i in range(0, len(sequence)):
        rate = phred33_to_rate(quality[i])
        if rnum.random() > rate:
            seq += sequence[i]
            qual += quality[i]
            continue
        seq += rnum.different_random_nt(sequence[i])
        qual += quality[i]
        #for del type we do nothing ... cause its not getting added
    return Fastq([fastq.name, seq, '+', qual])
コード例 #4
0
ファイル: emit.py プロジェクト: jason-weirather/Au-public
def do_quality_mismatch(fastq,rnum):
  sequence = fastq.seq
  quality = fastq.qual
  #five possible errors 3 base changes a deletion or insertion
  seq = ''
  qual = ''
  for i in range(0,len(sequence)):
    rate = phred33_to_rate(quality[i])
    if rnum.random() > rate:
      seq += sequence[i]
      qual += quality[i]
      continue
    seq += rnum.different_random_nt(sequence[i])
    qual += quality[i]
    #for del type we do nothing ... cause its not getting added
  return Fastq([fastq.name,seq,'+',qual])