def __init__(self, num, fname, verbose=None): sys.stderr.write('Note: MismatchDbSNP is considered *experimental*\n') self.num = int(num) self.fname = fname self.dbsnp = DBSNP(fname) if verbose == 'verbose': self.verbose = True else: self.verbose = False
def __init__(self, num, refname, dbsnpname): sys.stderr.write('Note: MismatchRefDbSNP is considered *experimental*\n') self.num = int(num) self.refname = refname self.dbsnp = DBSNP(dbsnpname) if not os.path.exists('%s.fai' % refname): pysam.faidx(refname) self.ref = pysam.Fastafile(refname)