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Mutalyzer
mutalyzer2
Commits
2c559f1d
Unverified
Commit
2c559f1d
authored
Aug 21, 2019
by
Mihai
Committed by
GitHub
Aug 21, 2019
Browse files
Merge pull request #485 from mutalyzer/entrez-api-key
Add support for NCBI E-utilities API key
parents
97a6309c
0ff4864f
Changes
2
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Inline
Side-by-side
mutalyzer/Retriever.py
View file @
2c559f1d
...
...
@@ -47,6 +47,8 @@ class Retriever(object):
if
not
os
.
path
.
isdir
(
settings
.
CACHE_DIR
):
os
.
mkdir
(
settings
.
CACHE_DIR
)
Entrez
.
email
=
settings
.
EMAIL
if
hasattr
(
settings
,
'ENTREZ_API_KEY'
):
Entrez
.
api_key
=
settings
.
ENTREZ_API_KEY
self
.
file_type
=
None
def
_name_to_file
(
self
,
name
):
...
...
mutalyzer/ncbi.py
View file @
2c559f1d
...
...
@@ -77,6 +77,8 @@ def _get_link_from_ncbi(source_db, target_db, match_link_name,
# below, so we cannot move to `accession.version` here. This is fine for
# now, but should be reconsidered at some point.
Entrez
.
email
=
settings
.
EMAIL
if
hasattr
(
settings
,
'ENTREZ_API_KEY'
):
Entrez
.
api_key
=
settings
.
ENTREZ_API_KEY
# If we are currently strictly matching on version, we can try again if
# no result is found. Otherwise, we just report failure.
...
...
@@ -343,6 +345,8 @@ def _get_snp_from_ncbi(rsid):
:return: response_text(str)
"""
Entrez
.
email
=
settings
.
EMAIL
if
hasattr
(
settings
,
'ENTREZ_API_KEY'
):
Entrez
.
api_key
=
settings
.
ENTREZ_API_KEY
try
:
response
=
Entrez
.
efetch
(
db
=
'snp'
,
id
=
rsid
[
2
:],
retmode
=
'xml'
)
...
...
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