def test_all():
from genelocator import get_genelocator
gl = get_genelocator(grch_build=38,
gencode_version=32,
only_codinglike_genetypes=True)
gene = gl.at('chr19', 1234)
assert gene == [('ENSG00000176695.8', '19', 107104, 117102, 'OR4F17')]
def main():
# TODO (future) Creating the tree is the slow step. A potential performance enhancement would be to allow searching
# for multiple positions from a single run of the command line (so we get many searches but pay startup penalty once)
args = parse_args()
gencode_version = args.version
try:
genelocator = get_genelocator(
args.build,
gencode_version=gencode_version,
common_genetypes_only=args.common_genetypes_only,
auto_fetch=args.auto_fetch)
except gene_exc.UnsupportedDatasetException:
logger.error('No source found for the requested dataset; exiting')
sys.exit(1)
for gene in genelocator.at(args.chromosome, args.position):
print('{chrom}\t{start}\t{end}\t{ensg}\t{symbol}'.format(**gene))
def build38finder():
# Mostly, tests are slow because of the time to build this tree. It's immutable, so only do this 1x per run
return get_genelocator('GRCh38',
gencode_version=32,
common_genetypes_only=True)
import json
import sqlite3
from flask import Blueprint, abort, jsonify, redirect, request, url_for
from genelocator import exception as gene_exc, get_genelocator # type: ignore
from zorp import readers # type: ignore
from .. import model
from ..api.format import (
TISSUES_PER_STUDY,
TISSUES_TO_SYSTEMS,
position_to_variant_id,
)
from .format import gencodeParser, gencodeTranscriptParser
gl = get_genelocator("GRCh38", gencode_version=32, coding_only=True)
views_blueprint = Blueprint("frontend", __name__, template_folder="templates")
@views_blueprint.route("/region/", methods=["GET"])
def region_view():
"""Region view"""
# The canonical form of this view uses start and end query params
# However, for convenience, some plots will want to link by a single position.
# We implement this as a simple redirect that otherwise preserves the query string.
pos = request.args.get("position", None)
if pos:
args = request.args.copy()
pos = int(pos)
args.pop("position")
def test_creates_locator_from_filepath(self):
"""This should work (measured by not raising an exception)"""
filepath = assets._get_cache_filepath('GRCh37', 32, 'common_genetypes')
get_genelocator(filepath)