trapes.py 文件源码

def writeReadsFileSE(mappedReadsDict, outReads, fastq):
    if fastq.endswith('.gz'):
        subprocess.call(['gunzip', fastq])
        newFq = fastq.replace('.gz','')
    else:
        newFq = fastq
    out = open(outReads, 'w')
    fqF = open(newFq, 'rU')
    for record in SeqIO.parse(fqF, 'fastq'):
        if record.id in mappedReadsDict:
            newRec = SeqRecord(record.seq, id = record.id, description = '')
            SeqIO.write(newRec,out,'fasta')
    out.close()
    fqF.close()
    if fastq.endswith('.gz'):
        subprocess.call(['gzip',newFq])