trapes.py 文件源码

python
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项目:TRAPeS 作者: YosefLab 项目源码 文件源码
def makeVDJBedDict(bed,idNameDict):
    fDict = {'Alpha':{'C':[],'V':[],'J':[]}, 'Beta':{'C':[],'V':[],'J':[]}}
    f = open(bed, 'r')
    l = f.readline()
    while l != '':
        lArr = l.strip('\n').split('\t')
        gID = lArr[3]
        gName = idNameDict[gID]
        chain = ''
        if (gName.startswith('TRA')):
            chain = 'Alpha'
        elif (gName.startswith('TRB')):
            chain = 'Beta'
        else:
            sys.stderr.write(str(datetime.datetime.now()) + ' Error! %s name is not alpha or beta chain, ignoring it\n' % gName)
            sys.stderr.flush()
        if gName.find('C') != -1:
            fDict[chain]['C'].append(l)
        elif gName.find('V') != -1:
            fDict[chain]['V'].append(l)
        elif gName.find('J') != -1:
            fDict[chain]['J'].append(l)
        l = f.readline()
    f.close()
    return fDict





# Creates a dictionary of ENSEMBL ID -> fasta sequence
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