datasets.py 文件源码

def validate(self):
        assert os.path.exists(self.bam), "missing bam file '{}' for sample '{}' and dataset '{}'".format(
                                         self.bam, self.sample.name, self.id)


    # @staticmethod
    # def from_longranger_dir(self, longranger_dir):
    #     fragments = os.path.join(longranger_dir,
    #         "PHASER_SVCALLER_CS/PHASER_SVCALLER/_REPORTER/"
    #         "REPORT_SINGLE_PARTITION/fork0/files/fragments.h5")

    #     bam = os.path.join(longranger_dir,
    #         "PHASER_SVCALLER_CS/PHASER_SVCALLER/ATTACH_PHASING/"
    #         "fork0/files/phased_possorted_bam.bam")

    #     phased_fragments = os.path.join(longranger_dir,
    #         "10XSARCOMAC1/PHASER_SVCALLER_CS/PHASER_SVCALLER/"
    #         "_SNPINDEL_PHASER/PHASE_SNPINDELS/fork0/files/"
    #         "fragment_phasing.tsv.gz")

    #     self.validate()

    #     return TenXDataset(bam, fragments, phased_fragments)

    # def load_phased_fragments(self, chrom=None, start=None, end=None):

    #     columns = ["chrom", "start_pos", "end_pos", "phase_set", "ps_start", 
    #                "ps_end", "bc", "h0", "h1", "hmix", "unkn"]

    #     try:
    #         tabix = pysam.TabixFile(self.phased_fragments)
    #         s = StringIO.StringIO("\n".join(tabix.fetch(chrom, start, end)))
    #         frags = pandas.read_table(s)
    #         frags.columns = columns
    #     except (IOError, ValueError):
    #         frags = pandas.DataFrame(columns=columns)

    #     return frags

    # def load_fragments(self, chrom=None, start=None, end=None):
    #     tabix = pysam.TabixFile()

        # try:
        #     fragments = utilities.read_data_frame(self.fragments)
        #     goodbcs = utilities.get_good_barcodes(fragments)
        #     fragments = fragments.loc[fragments["bc"].isin(goodbcs)]
        #     # fragments = fragments.loc[fragments["num_reads"]>5]
        #     if chrom is not None:
        #         fragments = fragments.loc[fragments["chrom"]==chrom]

        #     return fragments
        # except:
        #     logging.exception("Unable to load fragments from fragments file "
        #         "'{}'".format(self.fragments))
        #     raise