combine_bams.py 文件源码

def generate_sqlite_db(variants_to_process, temp_sqlite_db_path, sqlite_db_path):
    logging.info("populating sqlite database: " + temp_sqlite_db_path)
    if os.path.isfile(temp_sqlite_db_path):
        run("rm -f " + temp_sqlite_db_path)

    sqlite_db = peewee.SqliteDatabase(temp_sqlite_db_path, autocommit=False)
    class t(_SharedVariantPositionFields):
        n_expected_samples = peewee.IntegerField(index=True, null=True)
        n_available_samples = peewee.IntegerField(index=True, null=True)

        class Meta:
            database = sqlite_db
            indexes = (
                (('chrom', 'pos', 'ref', 'alt', 'het_or_hom_or_hemi'), True), # True means unique index
            )

    t.create_table(fail_silently=True)

    # copy the records from the Variant table used by generate_HC_bams.py
    sqlite_db.connect()
    with sqlite_db.atomic():
        for v in variants_to_process:  #Variant.select().where(Variant.finished==1).dicts():
            #shortcuts.model_to_dict(v)

            d = {
                'chrom': v.chrom, 'pos': v.pos, 'ref': v.ref, 'alt': v.alt, 'het_or_hom_or_hemi': v.het_or_hom_or_hemi,
                'n_expected_samples': v.n_expected_samples,
                'n_available_samples': v.n_available_samples,
            }

            # delete readviz_bam_paths as they're no longer relevant because the data from these is being combined into one bam file
            #print("INSERTING " + str(d))
            t.insert(**d).execute()
    sqlite_db.close()

    run("mv %s %s" % (temp_sqlite_db_path, sqlite_db_path))