Python get_baseQ示例

示例#1

文件： filter_reads_by_mean_qual.py 项目： brantp/short_read_analysis

def describe_fastq(filename):
    if preprocess_radtag_lane.smartopen(filename).read(1) == '@':
        lnum = 4
    else:
        lnum = 1
    baseQ = None
    fh = preprocess_radtag_lane.smartopen(filename)
    while baseQ is None:
        n,s,q = preprocess_radtag_lane.next_read_from_fh(fh)
        baseQ = preprocess_radtag_lane.get_baseQ(q)
    fh.close()
    return lnum,baseQ

示例#2

文件： read_quality_statistics.py 项目： brantp/short_read_analysis

def get_fastq_properties(fq):
    if smartopen(fq).read(1) == '@':
        lnum = 4
    else:
        lnum = 1
    print >> sys.stderr, 'fastq format lnum: %s' % lnum

    baseQ = None
    qfh = smartopen(fq)
    while baseQ is None:
        t,r,q = preprocess_radtag_lane.next_read_from_fh(qfh,lnum)
        baseQ = preprocess_radtag_lane.get_baseQ(q)
    qfh.close()
    print >> sys.stderr, 'fastq format baseQ: %s' % baseQ

    readlen = len(r)
    print >> sys.stderr, 'fastq format readlen: %s' % readlen

    return lnum,baseQ,readlen