Esempi in Python per ga4ghImportGlue

Esempio n. 1

File: server_benchmark.py Progetto: ga4gh/server

from __future__ import print_function
from __future__ import unicode_literals

import re
import time
import pstats
import argparse
import cProfile

import guppy

import glue

import ga4gh.schemas.protocol as protocol

glue.ga4ghImportGlue()
import ga4gh.server.backend as backend  # noqa
import ga4gh.server.datarepo as datarepo  # noqa


class HeapProfilerBackend(backend.Backend):
    def __init__(self, registryDb):
        repo = datarepo.SqlDataRepository(registryDb)
        repo.open(datarepo.MODE_READ)
        super(HeapProfilerBackend, self).__init__(repo)
        self.profiler = guppy.hpy()

    def startProfile(self):
        self.profiler.setrelheap()

    def endProfile(self):

Esempio n. 2

import argparse
import os
import shutil
import json
import pysam
import generate_gff3_db
import tempfile
import zipfile
import glob

import file_downloader

import ga4gh.common.utils as utils
import glue

glue.ga4ghImportGlue()

# We need to turn off QA because of the import glue
import ga4gh.server  # NOQA
import ga4gh.server.datarepo as datarepo  # NOQA
import ga4gh.server.datamodel.references as references  # NOQA
import ga4gh.server.datamodel.datasets as datasets  # NOQA
import ga4gh.server.datamodel.variants as variants  # NOQA
import ga4gh.server.datamodel.reads as reads  # NOQA
import ga4gh.server.datamodel.ontologies as ontologies  # NOQA
import ga4gh.server.datamodel.sequence_annotations as sequence_annotations  # NOQA
import ga4gh.server.datamodel.bio_metadata as biodata  # NOQA
import ga4gh.server.datamodel.genotype_phenotype_featureset as g2p_featureset  # NOQA
import ga4gh.server.datamodel.genotype_phenotype as g2p_associationset  # NOQA
import ga4gh.server.datamodel.rna_quantification as rna_quantification  # NOQA
import ga4gh.server.repo.rnaseq2ga as rnaseq2ga  # NOQA