Python process_consequence_type_fileの例

コード例 #1

def get_mappings(efo_mapping_file, snp_2_gene_file):
    mappings = SimpleNamespace()
    mappings.trait_2_efo, mappings.unavailable_efo = \
        load_efo_mapping(efo_mapping_file)

    mappings.consequence_type_dict = \
        CT.process_consequence_type_file(snp_2_gene_file)

    return mappings

コード例 #2

ファイル: clinvar_to_evidence_strings.py プロジェクト: cyenyxe/eva-cttv-pipeline

def get_mappings(efo_mapping_file, snp_2_gene_file):
    mappings = SimpleNamespace()
    mappings.trait_2_efo, mappings.unavailable_efo = \
        load_efo_mapping(efo_mapping_file)

    mappings.consequence_type_dict = \
        CT.process_consequence_type_file(snp_2_gene_file)

    return mappings

コード例 #3

def launch_pipeline(clinvar_xml_file, efo_mapping_file, gene_mapping_file,
                    ot_schema_file, dir_out):
    os.makedirs(dir_out, exist_ok=True)
    string_to_efo_mappings = load_efo_mapping(efo_mapping_file)
    variant_to_gene_mappings = CT.process_consequence_type_file(
        gene_mapping_file)
    report = clinvar_to_evidence_strings(string_to_efo_mappings,
                                         variant_to_gene_mappings,
                                         clinvar_xml_file,
                                         ot_schema_file,
                                         output_evidence_strings=os.path.join(
                                             dir_out,
                                             EVIDENCE_STRINGS_FILE_NAME))
    print(report.collate_report())
    report.write_unmapped_terms(dir_out)

コード例 #4

ファイル: test_clinvar.py プロジェクト: tskir/eva-opentargets

 def setUpClass(cls):
     cls.test_crm = get_test_record().measures[0]
     cls.consequence_type_dict = CT.process_consequence_type_file(
         config.snp_2_gene_file)

コード例 #5

 def setUpClass(cls):
     # A single example ClinVar record
     cls.test_crm = test_clinvar.get_test_record().measures[0]
     # Example result from the gene & functional consequence mapping pipeline for several variants
     cls.consequence_type_dict = CT.process_consequence_type_file(
         config.snp_2_gene_file)

コード例 #6

ファイル: test_evidence_strings.py プロジェクト: tskir/eva-opentargets

 def setUpClass(cls):
     cls.consequence_type_dict = CT.process_consequence_type_file(
         config.snp_2_gene_file)

コード例 #7

ファイル: test_clinvar_to_evidence_strings.py プロジェクト: cyenyxe/eva-cttv-pipeline

 def setUpClass(cls):
     cls.test_crm = test_clinvar.get_test_record().measures[0]
     cls.consequence_type_dict = CT.process_consequence_type_file(config.snp_2_gene_file)

コード例 #8

ファイル: test_clinvar_to_evidence_strings.py プロジェクト: EBIvariation/eva-opentargets

import unittest

import json
import os
import requests
import xml.etree.ElementTree as ElementTree

from eva_cttv_pipeline.clinvar_xml_utils import ClinVarTrait
from eva_cttv_pipeline.evidence_string_generation import clinvar_to_evidence_strings
from eva_cttv_pipeline.evidence_string_generation import consequence_type as CT
from tests.eva_cttv_pipeline.evidence_string_generation import config

EFO_MAPPINGS = clinvar_to_evidence_strings.load_efo_mapping(
    config.efo_mapping_file)
GENE_MAPPINGS = CT.process_consequence_type_file(config.snp_2_gene_file)


class GetMappingsTest(unittest.TestCase):
    @classmethod
    def setUpClass(cls):
        cls.efo_mappings = EFO_MAPPINGS
        cls.gene_mappings = GENE_MAPPINGS

    def test_efo_mapping(self):
        self.assertEqual(len(self.efo_mappings), 9)

        self.assertEqual(
            self.efo_mappings['renal-hepatic-pancreatic dysplasia 2'][0],
            ('http://www.orpha.net/ORDO/Orphanet_294415',
             'Renal-hepatic-pancreatic dysplasia'))
        self.assertEqual(