eutils – a simplified interface to NCBI E-Utilities¶
Contents¶
Introduction¶
eutils is a Python package to simplify searching, fetching, and parsing records from NCBI using their E-utilities interface.
Features¶
- simple Pythonic interface for searching and fetching
- automatic query rate throttling per NCBI guidelines
- optional sqlite-based caching of compressed replies
- “façades” that facilitate access to essential attributes in XML replies
Important Notes¶
- You are encouraged to browse issues. Please report any issues you find.
- Use a pip package specification to ensure stay within minor
releases for API stability. For example,
eutils >=0.1,<0.2.
Using eutils¶
Installation¶
The easiest way to install the eutils package is to use pre-build Python package from PyPI, like so:
$ pip install eutils
Consider using virtualenvwrapper or pyvenv to setup virtual environments before installing eutils.
Code that relies on eutils should specify a version bracket to ensure that eutils receives bug fixes but not updates that might break compatibility. In your package’s setup.py:
setup(
...
install_requires = [
'eutils>=0.4,<0.3',
],
...
)
Alternatively, you may install from source; please see Installation for Development for details.
Examples¶
Common setup¶
Instantiating an eutils eutils.Client is this easy:
>>> import eutils
# Initialize a client. This client handles all caching and query
# throttling
>>> ec = eutils.Client()
Fetching gene information¶
# search for tumor necrosis factor genes
# any valid NCBI query may be used
>>> esr = ec.esearch(db='gene',term='tumor necrosis factor')
# fetch one of those (gene id 7157 is human TNF)
>>> egs = ec.efetch(db='gene',id=7157)
# One may fetch multiple genes at a time. These are returned as an
# EntrezgeneSet. We'll grab the first (and only) child, which returns
# an instance of the Entrezgene class.
>>> eg = egs.entrezgenes[0]
# Easily access some basic information about the gene
>>> eg.hgnc, eg.maploc, eg.description, eg.type, eg.genus_species
('TP53', '17p13.1', 'tumor protein p53', 'protein-coding', 'Homo sapiens')
# get a list of genomic references
>>> [str(r) for r in eg.references]
['GeneCommentary(acv=NC_000017.11,type=genomic,heading=Reference GRCh38.p2 Primary Assembly,label=Chromosome 17 Reference GRCh38.p2 Primary Assembly)',
'GeneCommentary(acv=NG_017013.2,type=genomic,heading=None,label=RefSeqGene)',
'GeneCommentary(acv=NC_018928.2,type=genomic,heading=Alternate CHM1_1.1,label=Chromosome 17 Alternate CHM1_1.1)']
# Get all products defined on GRCh38
>>> [p.acv for p in eg.references[0].products]
[u'NM_001126112.2', u'NM_001276761.1', u'NM_000546.5',
u'NM_001276760.1', u'NM_001126113.2', u'NM_001276695.1',
u'NM_001126114.2', u'NM_001276696.1', u'NM_001126118.1',
u'NM_001126115.1', u'NM_001276697.1', u'NM_001126117.1',
u'NM_001276699.1', u'NM_001126116.1', u'NM_001276698.1']
# As a sample, grab the first product defined on this reference (order is arbitrary)
>>> mrna = eg.references[0].products[0]
>>> str(mrna)
'GeneCommentary(acv=NM_001126112.2,type=mRNA,heading=Reference,label=transcript variant 2)'
# mrna.genomic_coords provides access to the exon definitions on this
reference
>>> mrna.genomic_coords.gi, mrna.genomic_coords.strand
('568815581', -1)
>>> mrna.genomic_coords.intervals
[(7687376, 7687549), (7676520, 7676618), (7676381, 7676402),
(7675993, 7676271), (7675052, 7675235), (7674858, 7674970),
(7674180, 7674289), (7673700, 7673836), (7673534, 7673607),
(7670608, 7670714), (7668401, 7669689)]
# and the mrna has a product, the resulting protein:
>>> str(mrna.products[0])
'GeneCommentary(acv=NP_001119584.1,type=peptide,heading=Reference,label=isoform a)'
Fetch PubMed information¶
# search pubmed by author
>>> esr = c.esearch(db='pubmed', term='Nussbaum RL')
# fetch all of them
>>> paset = c.efetch(db='pubmed', id=esr.ids)
# paset represents PubmedArticleSet, a collection of
PubmedArticles. The major interface component is to iterate over
PubmedArticles with constructs like `for pa in paset: ...`. We
fetch the first PubmedArticle like this:
>>> pa = iter(paset).next()
PubmedArticle provides acccessors to essential data:
>>> pa.title
'High incidence of functional ion-channel abnormalities in a
consecutive Long QT cohort with novel missense genetic variants of
unknown significance.'
>>> pa.authors
[u'Steffensen AB', u'Refaat MM', u'David JP', u'Mujezinovic A',
u'Calloe K', u'Wojciak J', u'Nussbaum RL', u'Scheinman MM',
u'Schmitt N']
>>> pa.jrnl, pa.volume, pa.issue, pa.year
('Sci Rep', '5', None, '2015')
>>> pa.jrnl, pa.volume, pa.issue, pa.year, pa.pages
('Sci Rep', '5', None, '2015', '10009')
>>> pa.pmid, pa.doi, pa.pmc
('26066609', '10.1038/srep10009', '4464365')
Modules¶
Main Classes¶
-
class
eutils.Client(cache=False, api_key=None)[source]¶ Bases:
objectclass-based access to NCBI E-Utilities, returning Python classes with rich data accessors
Parameters: Raises: EutilsError – if cache file couldn’t be created
-
databases¶ list of databases available from eutils (per einfo query)
-
einfo(db=None)[source]¶ query the einfo endpoint
Parameters: db – string (optional) Return type: EInfo or EInfoDB object If db is None, the reply is a list of databases, which is returned in an EInfo object (which has a databases() method).
If db is not None, the reply is information about the specified database, which is returned in an EInfoDB object. (Version 2.0 data is automatically requested.)
-
-
class
eutils.QueryService(email='biocommons-dev@googlegroups.com', cache=False, default_args={'retmax': 250, 'retmode': 'xml', 'usehistory': 'y'}, request_interval=None, tool=None, api_key=None)[source]¶ Bases:
objectprovides throttled and cached querying of NCBI E-utilities services
QueryService has three functions:
- construct URLs appropriate for eutils endpoints
- throttle queries per NCBI guidelines
- cache results in persistent cache (sqlite)
QueryService works with any valid query arguments, passed as dictionaries.
Implemented interfaces:
- esearch
- efetch
- elink
- einfo
- esummary
Implementing other query modes should be straightforward.
- See also the NCBI’s Entrez Programming Utilities Help:
- http://www.ncbi.nlm.nih.gov/books/NBK25500/
Parameters: - email (str) – email of user (for abuse reports)
- cache (str) – if True, cache at ~/.cache/eutils-db.sqlite; if string, cache there; if False, don’t cache
- default_args (dict) – dictionary of query args that should accompany all requests
- request_interval (int or a callable returning an int) – seconds between requests; default: auto-select based on API key
- api_key (str) – api key assigned by NCBI
- tool (str) – name of client
Return type: Raises: OSError – if sqlite file can’t be opened
-
efetch(args)[source]¶ execute a cached, throttled efetch query
Parameters: args (dict) – dict of query items Returns: content of reply Return type: str Raises: EutilsRequestError – when NCBI replies, but the request failed (e.g., bogus database name)
-
einfo(args=None)[source]¶ execute a NON-cached, throttled einfo query
einfo.fcgi?db=<database>
Input: Entrez database (&db) or None (returns info on all Entrez databases)
Output: XML containing database statistics
Example: Find database statistics for Entrez Protein.
QueryService.einfo({“db”: “protein”})Equivalent HTTP request:
Parameters: args (dict) – dict of query items (optional) Returns: content of reply Return type: str Raises: EutilsRequestError – when NCBI replies, but the request failed (e.g., bogus database name)
-
elink(args)[source]¶ execute a cached, throttled elink query
Input: List of UIDs (&id); Source Entrez database (&dbfrom); Destination Entrez database (&db)
Output: XML containing linked UIDs from source and destination databases
Example: Find one set of Gene IDs linked to nuccore GIs 34577062 and 24475906
QueryService.elink({“dbfrom”: “nuccore”, “db”: “gene”, “id”: “34577062,24475906”})Equivalent HTTP request:
Parameters: args (dict) – dict of query items containing at least the “db”, “dbfrom”, and “id” keys. Returns: content of reply Return type: str Raises: EutilsRequestError – when NCBI replies, but the request failed (e.g., bogus database name)
-
esearch(args)[source]¶ execute a cached, throttled esearch query
Parameters: args (dict) – dict of query items, containing at least “db” and “term” keys Returns: content of reply Return type: str Raises: EutilsRequestError – when NCBI replies, but the request failed (e.g., bogus database name)
-
esummary(args)[source]¶ execute a cached, throttled esummary query
Input: List of UIDs (&id); Entrez database (&db)
Output: XML document summary for requested ID(s) [comma-separated]
Example:
QueryService.esummary({ “db”: “medgen”, “id”: 134 })Equivalent HTTP request:
Parameters: args (dict) – dict of query items containing at least “db” and “id” keys. Returns: content of reply Return type: str Raises: EutilsRequestError – when NCBI replies, but the request failed (e.g., bogus database name)
Exceptions¶
-
class
eutils.EutilsError[source]¶ Bases:
ExceptionBase class for all Eutils exceptions, and also used to raise general exception.
-
class
eutils.EutilsNCBIError[source]¶ Bases:
eutils._internal.exceptions.EutilsErrorRaised when NCBI returns data that appears to be incorrect or invalid.
-
class
eutils.EutilsNotFoundError[source]¶ Bases:
eutils._internal.exceptions.EutilsErrorRaised when the requested data is not available. (Used only by the
eutils.sketchy.clientxinterface currently.)
Experimental¶
-
class
eutils.sketchy.clientx.ClientX(cache=False, api_key=None)[source]¶ Bases:
eutils._internal.client.Clientwarning This class is subject to rapid development and api changes.
A subclass of eutils.client.Client that provides specific lookup functions.
This functionality is in a separate class because the API is experimental.
Parameters: Raises: EutilsError – if cache file couldn’t be created
-
fetch_gbseq_by_ac(acv)¶
-
Contributing¶
Development occurs in the default branch. Please work in feature branches or bookmarks from the default branch. Feature branches should be named for the eutils issue they fix, as in 121-update-xml-facades. When merging, use a commit message like “closes #121: update xml facades to new-style interface”. (“closes #n” is recognized automatically and closes the ticket upon pushing.)
The included Makefile automates many tasks. In particular, make develop prepares a development environment and make test runs unittests. (Please run tests before committing!)
Again, thanks for your contributions.
Development¶
This section is intended for developers seeking to extend the eutils package. You should be familiar with the architecture, conventions, and basic functionality elsewhere in this documentation.
Get Cozy with make¶
The eutils package includes a GNU Makefile that aids nearly all developer tasks. It subsumes much of the functionality in setup.py. While using the Makefile isn’t required to develop, it is the official way to invoke tools, tests, and other development features. Type make for eutils-specific help.
Some of the key targets are:
develop: Prepare the directory for local development. install: Install eutils (as with python setup.py install). test: Run the default test suite clean, cleaner, cleanest: Remove extraneous files, leaving a directory in various states of tidiness. docs: Make the sphinx docs in doc/build/html/. upload, upload_docs: Upload package to PyPI or docs to pythonhosted.org.
Installation for Development¶
You will need Mercurial to clone the eutils repository.
$ hg clone ssh://hg@bitbucket.org/biocommons/eutils
$ cd eutils
$ make develop
Submitting Patches¶
Yes! We’ll be thrilled to have your contributions!
The preferred way to submit a patch is by forking the project on BitBucket, commiting your changes there, then sending a pull request.
If you have a really worthwhile patch, we’ll probably accept a diff-formatted patch, but that’ll make it harder for us and impossible for you to get credit.
Developing and Contributing to eutils¶
Fork the project at https://bitbucket.org/biocommons/eutils/
Clone the project locally with:
$ hg clone https://bitbucket.org/<your_username>/eutils
Create a virtualenv:
$ mkvirtualenv eutils
mkvirtualenv is part of the virtualenvwrapper package. Python3 users should prefer pyvenv.
Prepare your environment:
$ make develop
(The Makefile in eutils wraps functionality in setup.py, and also
provides many useful utilitarian rules. Type make to see a list of
targets.)
Create an issue at https://github.com/biocommons/eutils/issues/ for the feature you want to work on. This helps tracking for changelogs.
Create a mercurial bookmark for your feature. Please name the bookmark like 141-implement-caching (where 141 is the issue number).
Code away, then commit and push:
$ hg commit -m 'fixes #141: implemented caching' $ hg push
If you’d like to contribute back, create a pull request.
ChangeLog¶
0.6 Series¶
0.6.0 (2019-12-17)¶
Changes since 0.5.2 (2019-05-15).
Special Attention¶
Support for Python 2.7 has been dropped.
Deprecations¶
Bug Fixes¶
New Features¶
Other Changes¶
Internal and Developer Changes¶
- Add .deepsource.toml, Fix issues raised by DeepSource (#163) [db41c8b] (Mohit Solanki)
- Dropped python 2.7 support [3e53fa2] (Reece Hart)
- Closes #166: Remove six and _internal/compat.py [b5d4e84] (Reece Hart)
- Sync with current biocommons conventions: use setup.cfg, use src/, Makefile updates, drop req files [a232d9b] (Reece Hart)
- Add support for testing on Python 3.8 on travis and tox [0e6e2f0] (Reece Hart)
0.5 Series¶
0.5.0 (2018-11-19)¶
Changes since 0.4.1 (2018-10-10).
Special Attention¶
Support for Python < 3.6 will be dropped on 2019-03-31. This release will issue warnings when imported by an python version < 3.6. See https://github.com/biocommons/org/wiki/Migrating-to-Python-3.6
New Features¶
Internal and Developer Changes¶
- removed py 3.5 from travis config; updated badges in README [5ab476c]
- sync project files with bioutils; use travis stages for test+deploy [2a2222e]
- deprecate python < 3.6; see https://github.com/biocommons/org/wiki/Migrating-to-Python-3.6 [57c41cc]
0.4 Series¶
Important
Clients should import only from eutils (e.g., import
eutils). Importing from submodules (e.g., import
eutils.client) will fail in the 0.5 release.
0.4.1 (2018-10-11)¶
Changes since 0.4.0 (2018-05-28).
0.4.0 (2018-05-28)¶
Changes since 0.3.2 (2017-11-02).
Special Attention¶
Removed time-based throttling and added support for NCBI API keys. Without an API key, NCBI returns an error if clients make more than 3 requests/second. With an API, clients may make 10 requests/second. See https://www.ncbi.nlm.nih.gov/books/NBK25497/. The API key may be passed as argument to Client and QueryService.
0.3 Series¶
0.2 Series¶
0.2.4 (2017-02-21)¶
Changes since 0.2.3 (2017-02-03).
Special Attention¶
Deprecations¶
Bug Fixes¶
New Features¶
Other Changes¶
Internal and Developer Changes¶
- Implemented wheel support
0.2.3 (2017-02-03)¶
Changes since 0.2.2 (2016-12-10).
0.2.2 (2016-12-10)¶
Changes since 0.2.1 (2016-10-19).
License¶
eutils is released under the Apache License 2.0, the text of which appears below:
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