Releases: bebatut/enasearch
Releases · bebatut/enasearch
Release: 0.2.0
Release: 0.1.1
Fix:
- Error handling with a user-friendly output
- All returnable fields as default
- Comma-separated support for fields
- Ugly output of the CLI
Add
- Code coverage checking
- Code health checking
- Tests for CLI
Release: 0.0.6
Fix:
- Support
-has well as--help - Add
--version - Remove (strange) boolean checking
Release: 0.0.5
Increase version
First version of ENASearch
ENASearch is a Python library for interacting with ENA's API.
Usage
ENASearch is easy to use
$ enasearch --help
Usage: enasearch [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
get_analysis_fields Get analysis fields
get_display_options Get display options
get_download_options Get download options
get_filter_fields Get filter fields
get_filter_types Get filter types
get_results Get list of results
get_returnable_fields Get returnable fields
get_run_fields Get run fields
get_sortable_fields Get sortable fields
get_taxonomy_results Get list of taxonomy results
retrieve_analysis_report Retrieve analysis report
retrieve_data Retrieve ENA data
retrieve_run_report Retrieve run report
retrieve_taxons Retrieve ENA taxon data
search_data Search data
$ enasearch search_data --help
Usage: enasearch search_data [OPTIONS]
Search data given a query
Options:
--query TEXT Query string, made up of filtering conditions,
joined by logical ANDs , ORs and NOTs and bound
by double quotes; the filter fields for a query
are accessible with get_filter_fields and the type
of filters with get_ filter_types
--result TEXT Id of a result (accessible with get_results)
--display TEXT Display option to specify the display format
(accessible with get_ display_options)
--download TEXT (Optional) Download option to specify that records
are to be saved in a file (used with file
option, list accessible with get_download_
options)
--file PATH (Optional) File to save the content of the search
(used with download option)
--fields TEXT (Optional, Multiple) Fields to return (accessible
with get_returnable _fields, used only for report
as display value)
--sortfields TEXT (Optional, Multiple) Fields to sort the results
(accessible with get_ sortable_fields, used only
for report as display value)
--offset INTEGER RANGE (Optional) First record to get (used only for
display different of fasta and fastq
--length INTEGER RANGE (Optional) Number of records to retrieve (used only
for display different of fasta and fastq
--help Show this message and exit.
It can also be used as a Python library:
>>> import enasearch
>>> enasearch.retrieve_data(
ids="A00145",
display="fasta",
download=None,
file=None,
offset=0,
length=100000,
subseq_range="3-63",
expanded=None,
header=None)
[SeqRecord(seq=Seq('GAAGGAAGGTCTTCAGAGAACCTAGAGAGCAGGTTCACAGAGTCACCCACCTCA...GCC', SingleLetterAlphabet()), id='ENA|A00145|A00145.1', name='ENA|A00145|A00145.1', description='ENA|A00145|A00145.1 B.taurus BoIFN-alpha A mRNA : Location:3..63', dbxrefs=[])]
The information extracted from ENA can be in several formats: HTML, Text, XML, FASTA, FASTQ, ... XML outputs are transformed in a Python dictionary using xmltodict and the FASTA and FASTQ into SeqRecord objects using BioPython <http://biopython.org/wiki/Biopython>_.
Installation
To install ENASearch, simply:
$ pip install enasearch
Tests
ENASearch comes with tests:
$ make test
Generate the data descriptions
To run, ENASearch needs some data from ENA to describe how to query ENA.
Currently, such information is manually extracted into CSV files in the data directory. Python objects are generated from these CSV files with
$ python src/serialize_ena_data_descriptors.py