def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation."""
for clinsig_obj in variant_obj['clnsig']:
# The clinsig objects allways have a accession
if isinstance(clinsig_obj['accession'], int):
# New version
link = "https://www.ncbi.nlm.nih.gov/clinvar/variation/{}"
else:
# Old version
link = "https://www.ncbi.nlm.nih.gov/clinvar/{}"
human_str = 'not provided'
if clinsig_obj.get('value'):
try:
# Old version
int(clinsig_obj['value'])
human_str = CLINSIG_MAP.get(clinsig_obj['value'], 'not provided')
except ValueError:
# New version
human_str = clinsig_obj['value']
clinsig_obj['human'] = human_str
clinsig_obj['link'] = link.format(clinsig_obj['accession'])
yield clinsig_obj
def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation."""
for clinsig_obj in variant_obj['clnsig']:
human_str = CLINSIG_MAP.get(clinsig_obj['value'], 'not provided')
clinsig_obj['human'] = human_str
clinsig_obj['link'] = ("https://www.ncbi.nlm.nih.gov/clinvar/{}"
.format(clinsig_obj['accession']))
yield clinsig_obj
def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation.
The clinical significance from ACMG are stored as numbers. These needs to be converted to human
readable format. Also the link to the accession is built
Args:
variant_obj(scout.models.Variant)
Yields:
clinsig_objs(dict): {
'human': str,
'link': str
}
"""
for clinsig_obj in variant_obj.get("clnsig", []):
# The clinsig objects allways have a accession
if not "accession" in clinsig_obj:
continue
# Old version
link = "https://www.ncbi.nlm.nih.gov/clinvar/{}"
if isinstance(clinsig_obj["accession"], int):
# New version
link = "https://www.ncbi.nlm.nih.gov/clinvar/variation/{}"
human_str = "not provided"
clinsig_value = clinsig_obj.get("value")
if clinsig_value:
try:
# Old version
int(clinsig_value)
human_str = CLINSIG_MAP.get(clinsig_value, "not provided")
except ValueError:
# New version
human_str = clinsig_value
clinsig_obj["human"] = human_str
clinsig_obj["link"] = link.format(clinsig_obj["accession"])
yield clinsig_obj
# -*- coding: utf-8 -*-
import decimal
from flask_wtf import FlaskForm
from wtforms import (BooleanField, DecimalField, Field, TextField, SelectMultipleField,
HiddenField, IntegerField, SubmitField)
from wtforms.widgets import TextInput
from flask_wtf.file import FileField
from scout.constants import (CLINSIG_MAP, FEATURE_TYPES, GENETIC_MODELS, SO_TERMS,
SPIDEX_LEVELS, SV_TYPES)
CLINSIG_OPTIONS = list(CLINSIG_MAP.items())
FUNC_ANNOTATIONS = [(term, term.replace('_', ' ')) for term in SO_TERMS]
REGION_ANNOTATIONS = [(term, term.replace('_', ' ')) for term in FEATURE_TYPES]
SV_TYPE_CHOICES = [(term, term.replace('_', ' ').upper()) for term in SV_TYPES]
SPIDEX_CHOICES = [(term, term.replace('_', ' ')) for term in SPIDEX_LEVELS]
class TagListField(Field):
widget = TextInput()
def _value(self):
if self.data:
return ', '.join(self.data)
else:
return ''
def process_formdata(self, valuelist):
if valuelist:
self.data = [x.strip() for x in valuelist[0].split(',') if x.strip()]
else:
def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation."""
for clinsig_obj in variant_obj['clnsig']:
human_str = CLINSIG_MAP.get(clinsig_obj.value, 'not provided')
yield clinsig_obj, human_str