def setup(self, f):
self.assembly = self.input_assembly
if self.assembly == 'hg19':
self.wgs = get_wgs_reader(assembly='hg19')
self.refversion = 'hg19'
elif self.assembly == 'hg38':
self.wgs = get_wgs_reader(assembly='hg38')
self.refversion = 'hg38'
def __init__(self, args=None, status_writer=None):
args = args if args else sys.argv
self.status_writer = status_writer
self.input_paths = []
self.input_files = []
self.input_format = None
self.logger = None
self.crv_writer = None
self.crs_writer = None
self.crm_writer = None
self.crl_writer = None
self.primary_converter = None
self.converters = {}
self.possible_formats = []
self.ready_to_convert = False
self.cmd_args = None
self.output_dir = None
self.output_base_fname = None
self.pipeinput = False
self.chromdict = {
'chrx': 'chrX',
'chry': 'chrY',
'chrMT': 'chrM',
'chrMt': 'chrM',
'chr23': 'chrX',
'chr24': 'chrY'
}
self._parse_cmd_args(args)
self._setup_logger()
self.vtracker = VTracker(deduplicate=not (self.unique_variants))
self.wgsreader = cravat.get_wgs_reader(assembly='hg38')
def setup (self):
self.filenames = []
self.filename = None
self.filename_prefix = None
if self.savepath == None:
self.filename_prefix = "cravat_result"
else:
self.filename_prefix = self.savepath
self.headers = {}
self.dataframe_cols = {}
self.dataframe_colnos = {}
self.dataframe_headers = {}
self.colno_to_colname = {}
self.levels_to_write = self.get_standardized_module_option(self.confs.get('pages',['variant']))
self.filename_postfix = 'RData'
self.data = {}
self.wgs_reader = cravat.get_wgs_reader('hg38')
def __init__(self, *inargs, **inkwargs):
self._parse_cmd_args(inargs, inkwargs)
self.logger = None
self.crv_writer = None
self.crs_writer = None
self.crm_writer = None
self.crl_writer = None
self.primary_converter = None
self.converters = {}
self.possible_formats = []
self.ready_to_convert = False
self.chromdict = {
'chrx': 'chrX',
'chry': 'chrY',
'chrMT': 'chrM',
'chrMt': 'chrM',
'chr23': 'chrX',
'chr24': 'chrY'
}
self._setup_logger()
self.vtracker = VTracker(deduplicate=not (self.unique_variants))
self.wgsreader = cravat.get_wgs_reader(assembly='hg38')
def __init__(self, *inargs, **inkwargs):
self._parse_cmd_args(inargs, inkwargs)
self.logger = None
self.crv_writer = None
self.crs_writer = None
self.crm_writer = None
self.crl_writer = None
self.primary_converter = None
self.converters = {}
self.possible_formats = []
self.ready_to_convert = False
self.chromdict = {
"chrx": "chrX",
"chry": "chrY",
"chrMT": "chrM",
"chrMt": "chrM",
"chr23": "chrX",
"chr24": "chrY",
}
self._setup_logger()
self.vtracker = VTracker(deduplicate=not (self.unique_variants))
self.wgsreader = cravat.get_wgs_reader(assembly="hg38")
self.crs_def = constants.crs_def.copy()
def setup(self, f):
self.wgs = get_wgs_reader(assembly='hg19')
self.good_vars = set(['T', 'C', 'G', 'A'])
import time
from concurrent.futures import ProcessPoolExecutor
from cravat import get_live_annotator, get_live_mapper
from cravat.config_loader import ConfigLoader
import requests
import oyaml
import datetime
from pyliftover import LiftOver
import cravat
live_modules = {}
live_mapper = None
module_confs = {}
modules_to_run_ordered = []
oncokb_cache = {}
wgsreader = cravat.get_wgs_reader(assembly='hg38')
async def test(request):
return web.json_response({'result': 'success'})
async def get_live_annotation_post(request):
queries = await request.post()
response = await get_live_annotation(queries)
return web.json_response(response)
async def get_live_annotation_get(request):
queries = request.rel_url.query
response = await get_live_annotation(queries)
import aiosqlite
import os
import cravat
import cravat.admin_util as au
info = au.get_local_module_info('go')
path = info.directory
wgr = cravat.get_wgs_reader()
async def get_data (queries):
response = {}
dbpath = queries['dbpath']
conn = await aiosqlite.connect(dbpath)
cursor = await conn.cursor()
table = 'variant'
query = 'select name from sqlite_master where type="table" and name="' + table + '"'
await cursor.execute(query)
r = await cursor.fetchone()
from_str = ' from variant '
query = 'select base__chrom, base__pos, base__ref_base, base__alt_base '
query += from_str
await cursor.execute(query)
# get all triplets with 'A' in the middle
tripletDataA = [a + 'A' + c for a in ['A', 'T', 'G', 'C'] for c in ['A', 'T', 'G', 'C']]
# get all triplets with 'G' in the middle