Python read_calc_variations示例

示例#1

文件： filter.py 项目： willemdek11/tools-iuc

    def filter(self, bam, read):
        if read.is_unmapped:
            return False

        if read_calc_mismatches(read) <= self.num:
            return True

        chrom = bam.getrname(read.tid)

        mm = 0
        snps = 0

        for op, pos, seq in read_calc_variations(read):
            if not self.dbsnp.is_valid_variation(chrom, op, pos, seq,
                                                 self.verbose):
                mm += 1
            else:
                snps += 1

        if mm > self.num:
            return False

        if snps:
            read.tags = read.tags + [('ZS', snps)]

        return True

示例#2

文件： filter.py 项目： pjbriggs/tools-iuc

    def filter(self, bam, read):
        if read.is_unmapped:
            return False

        if read_calc_mismatches(read) <= self.num:
            return True

        chrom = bam.getrname(read.tid)

        mm = 0
        snps = 0

        for op, pos, seq in read_calc_variations(read):
            if not self.dbsnp.is_valid_variation(chrom, op, pos, seq, self.verbose):
                mm += 1
            else:
                snps += 1

        if mm > self.num:
            return False

        if snps:
            read.tags = read.tags + [('ZS', snps)]

        return True