trapes.py 文件源码

def addSegmentToJunctionFileSE(vSeg,jSeg,cSeg,out,fastaDict, bases, idNameDict):
    vSeq = fastaDict[vSeg]
    if jSeg != 'NA':
        jName = idNameDict[jSeg]
        jSeq = fastaDict[jSeg]
    else:
        jSeq = ''
        jName = 'NoJ'
    if cSeg != 'NA':
        cName = idNameDict[cSeg]
        cSeq = fastaDict[cSeg]
    else:
        cName = 'NoC'
        cSeq = ''
    jcSeq = jSeq + cSeq
    lenSeg = min(len(vSeq),len(jcSeq))
    if bases != -10:
        if lenSeg < bases:
            sys.stdout.write(str(datetime.datetime.now()) + ' Bases parameter is bigger than the length of the V or J segment, taking the length' \
                    'of the V/J segment instead, which is: ' + str(lenSeg) + '\n')
            sys.stdout.flush()
        else:
            lenSeg = bases
    jTrim = jcSeq[:lenSeg]
    vTrim = vSeq[-1*lenSeg:]
    junc = vTrim + jTrim
    recordName = vSeg + '.' + jSeg + '.' + cSeg + '(' + idNameDict[vSeg] + '-' + jName + '-' + cName + ')'
    record = SeqRecord(Seq(junc,IUPAC.ambiguous_dna), id = recordName, description = '')
    SeqIO.write(record,out,'fasta')