{command} build chromosome pos1 pos2 [tolerant]
build: Human Genome reference build, e.g. 'hg19'.
chromosome: Chromosome name, e.g. 'chr12'.
pos1: Beginning of chromosomal region, e.g. 230838269.
pos2: End of chromosomal region, e.g. 230938269.
tolerant: Optionally set region matching to be tolerant, e.g. 1.
The transcript information is retrieved from the Mutalyzer SOAP web service
and printed to standard output.
"""
from __future__ import unicode_literals
from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
import sys
from suds.client import Client
from mutalyzer.util import format_usage
WSDL_LOCATION = 'http://127.0.0.1:8081/?wsdl'
def main(build, chromosome, pos1, pos2, tolerant=0):
"""
Get extended transcript information and print this to standard output.
"""
service = Client(WSDL_LOCATION, cache=None).service
Usage:
{command} transcript variant [build]
transcript: Transcript accession number, e.g. 'NM_001008541.1'.
variant: Variant to map, e.g. 'g.112039014G>T'.
build: Human genome build, 'hg18' or 'hg19' (default: 'hg19').
The mapping information is retrieved from the Mutalyzer SOAP web service and
printed to standard output.
"""
from __future__ import unicode_literals
from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
import sys
from suds.client import Client
from mutalyzer.util import format_usage
WSDL_LOCATION = 'http://127.0.0.1:8081/?wsdl'
def main(transcript, variant, build='hg19'):
"""
Get mapping information and print it to standard output.
"""
service = Client(WSDL_LOCATION, cache=None).service
"""
Run the Mutalyzer syntaxchecker on a variant description.
Usage:
{command} description
description: Variant description to check.
The syntaxchecker results are retrieved from the Mutalyzer SOAP web service
and printed to standard output.
"""
from __future__ import unicode_literals
from mutalyzer.util import monkey_patch_suds
monkey_patch_suds()
import sys
from suds.client import Client
from mutalyzer.util import format_usage
WSDL_LOCATION = 'http://127.0.0.1:8081/?wsdl'
def main(description):
"""
Run the Mutalyzer syntaxchecker and print results to standard output.
"""
service = Client(WSDL_LOCATION, cache=None).service
result = service.checkSyntax(description)
Usage:
{command} transcript
transcript: Transcript accession number, e.g. 'NM_002001.2'.
The transcript information is retrieved from the Mutalyzer SOAP web service
and printed to standard output.
"""
from __future__ import unicode_literals
from mutalyzer.util import monkey_patch_suds
monkey_patch_suds()
import sys
from suds.client import Client
from mutalyzer.util import format_usage
WSDL_LOCATION = "http://127.0.0.1:8081/?wsdl"
def main(transcript):
"""
Get transcript information and print it to standard output.
"""
service = Client(WSDL_LOCATION, cache=None).service
