fasta.py 文件源码

def __init__(self,fastafile=None):
        '''initialize object, lowercase in sequence is automatically converted into uppercase'''
        self.seqs={}
        self.IDs=[]
        self.transtab = maketrans("ACGTNX","TGCANX")
        self.filename = fastafile
        tmpseq=''
        if fastafile is not None:
            for line in open(fastafile,'r'):
                line=line.strip(' \n')
                if line.startswith('>'):
                    if(tmpseq):
                        self.seqs[name]=tmpseq
                    name=line[1:]
                    tmpseq =''
                    self.IDs.append(name)
                    print >>sys.stderr,"\tloading "+name+' ...'
                else:
                    tmpseq += line.upper()
            self.seqs[name]=tmpseq