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Mutalyzer
mutalyzer2
Commits
fd58a127
Unverified
Commit
fd58a127
authored
Aug 19, 2019
by
Mihai
Committed by
GitHub
Aug 19, 2019
Browse files
Merge pull request #483 from mutalyzer/fix-482
Update HGVS descriptions retrieval for SNP converter (
#482
)
parents
bffd1999
4d0648e1
Changes
6
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.travis.yml
View file @
fd58a127
# Validate this file using http://lint.travis-ci.org/
dist
:
xenial
language
:
python
sudo
:
false
cache
:
pip
...
...
@@ -6,7 +7,9 @@ python: "2.7"
addons
:
apt_packages
:
swig
postgresql
:
"
9.4"
services
:
redis-server
services
:
-
redis-server
-
mysql
before_install
:
-
CFLAGS=-O0 pip install -r requirements.txt
-
pip install psycopg2
...
...
mutalyzer/ncbi.py
View file @
fd58a127
...
...
@@ -394,7 +394,7 @@ def rsid_to_descriptions(rsid, output):
try
:
# Parse the output.
doc
=
minidom
.
parseString
(
response_text
)
rs
=
doc
.
getElementsByTagName
(
'
Rs'
)[
0
]
docsum
=
doc
.
getElementsByTagName
(
'
DOCSUM'
)[
0
].
childNodes
[
0
].
data
except
expat
.
ExpatError
:
# TODO: Log error.
raise
ServiceError
()
...
...
@@ -402,7 +402,11 @@ def rsid_to_descriptions(rsid, output):
# The expected root element is not present, this has also been
# observed as a response for non-existing rs#.
output
.
addMessage
(
__file__
,
2
,
'EENTREZ'
,
'Non existing %s in the DB or no root element.'
%
rsid
)
'Non existing %s in the DB or no root element.'
%
rsid
)
return
[]
return
[
hgvs
.
lastChild
.
data
for
hgvs
in
rs
.
getElementsByTagName
(
'hgvs'
)]
for
part
in
docsum
.
split
(
'|'
):
if
part
.
startswith
(
'HGVS='
):
return
part
.
split
(
'='
)[
1
].
split
(
','
)
return
[]
tests/data/rs9919552.xml.bz2
View file @
fd58a127
No preview for this file type
tests/test_scheduler.py
View file @
fd58a127
...
...
@@ -76,18 +76,17 @@ def test_snp_converter():
"""
snps
=
[
'rs9919552'
]
expected
=
[[
'rs9919552'
,
'|'
.
join
([
'NC_000011.9:g.111959625C>T'
,
'NG_012337.2:g.7055C>T'
,
'NG_033145.1:g.2898G>A'
,
'NM_001276503.1:c.169+928C>T'
,
'NM_001276504.1:c.87C>T'
,
'NM_001276506.1:c.204C>T'
,
'|'
.
join
([
'NC_000011.10:g.112088901C>T'
,
'NC_000011.9:g.111959625C>T'
,
'NG_012337.3:g.7055C>T'
,
'NM_003002.4:c.204C>T'
,
'NM_003002.3:c.204C>T'
,
'NP_001263433.1:p.Ser29='
,
'NP_001263435.1:p.Ser68='
,
'NP_002993.1:p.Ser68='
,
'NM_001276506.2:c.204C>T'
,
'NM_001276506.1:c.204C>T'
,
'NM_001276504.2:c.87C>T'
,
'NM_001276504.1:c.87C>T'
,
'NR_077060.1:n.288C>T'
,
'N
T
_033
899.8:g.15522041C>T
'
])]]
'N
G
_033
145.1:g.2898G>A
'
])]]
# Patch Bio.Entrez.efetch to return dbSNP record for rs9919552.
def
mock_efetch
(
*
args
,
**
kwargs
):
...
...
tests/test_services_soap.py
View file @
fd58a127
...
...
@@ -445,9 +445,8 @@ def test_getdbsnpdescriptions(api):
r
=
api
(
'getdbSNPDescriptions'
,
'rs9919552'
)
assert
'NC_000011.9:g.111959625C>T'
in
r
.
string
assert
'NG_012337.
2
:g.7055C>T'
in
r
.
string
assert
'NG_012337.
3
:g.7055C>T'
in
r
.
string
assert
'NM_003002.3:c.204C>T'
in
r
.
string
assert
'NP_002993.1:p.Ser68='
in
r
.
string
@
pytest
.
mark
.
usefixtures
(
'hg19_transcript_mappings'
)
...
...
tests/test_website.py
View file @
fd58a127
...
...
@@ -364,9 +364,8 @@ def test_snp_converter_valid(website):
assert
'0 Errors'
in
r
.
data
assert
'0 Warnings'
in
r
.
data
assert
'NC_000011.9:g.111959625C>T'
in
r
.
data
assert
'NG_012337.
2
:g.7055C>T'
in
r
.
data
assert
'NG_012337.
3
:g.7055C>T'
in
r
.
data
assert
'NM_003002.3:c.204C>T'
in
r
.
data
assert
'NP_002993.1:p.Ser68='
in
r
.
data
def
test_snp_converter_invalid
(
website
):
...
...
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