https://github.com/moongoal/www-uniprot
WWW::UniProt perl module for UniProt search and data retrieval
https://github.com/moongoal/www-uniprot
Last synced: about 2 months ago
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WWW::UniProt perl module for UniProt search and data retrieval
- Host: GitHub
- URL: https://github.com/moongoal/www-uniprot
- Owner: moongoal
- License: other
- Created: 2015-06-04T21:11:08.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2015-06-12T08:27:38.000Z (about 11 years ago)
- Last Synced: 2025-03-12T06:41:43.010Z (over 1 year ago)
- Language: Perl
- Size: 164 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: ChangeLog
- License: LICENSE
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README
# NAME
WWW::UniProt - UniProt search and data retrieval module
# SYNOPSIS
use WWW::UniProt;
$fasta = WWW::UniProt::prot_data 'Q8JJY4'; # Grab FASTA
# DESCRIPTION
This module allows programmatic access the UniProt database.
Currently two subroutines are available:
## prot\_data($protname)
## prot\_data($protname, \\%opts)
This subroutine retrieves information about a protein from the UniProt
database. It accepts one mandatory argument `$query` and one optional
`\%opts`. The `$protname` argument is a string representing the code of the
protein about which you want to retrieve information from UniProt (i.e.
'Q8JJY4'). The `\%opts` argument is an optional reference to a hash of
optional arguments.
### Optional arguments
- dataset
A string representing the database to search (i.e. 'uniprot', 'uniref',
'uniparc'; defaults to 'uniprot')
- format
A string representing the format of the data to retrieve (i.e. 'fasta', 'xml',
'rdf', etc...; defaults to 'fasta')
- include
A boolean value representing whether referenced datasets should be included
inside the RDF/XML files (defaults to 0)
### Return value
This subroutine returns a string representing the data as returned by UniProt
or `undef` if the data could not be retrieved.
## search($query)
## search($query, \\%otps)
This subroutine performs a search on UniProt. It accepts one mandatory argument
`$query` and one optional `\%opts`. The `$query` argument is a query string
that will be used to search UniProt (i.e. 'myosin', 'amoeba', etc...). The
`\%opts` argument is an optional reference to a hash of optional arguments.
### Optional arguments
- limit
An integer representing the max number of entries to retrieve
- offset
An integer representing the number of entries to skip
- columns
An array reference representing the columns to retrieve
- \*
Any other value will be inserted as is in the url in the form KEY=VALUE
For a list of all the UniProt query options, refer to
[http://www.uniprot.org/help/programmatic\_access](http://www.uniprot.org/help/programmatic_access).
### Return value
This subroutine returns an array of records returned by the performed search or
`undef` if the request could not be satisfied. Each element is a hash
reference in which each key is the name of one of the requested columns and
each value is the value of that column for that record.
# CONNECTION SETTINGS
As this module uses **LWP** to connect to UniProt, please refer to its
documentation for information about connection settings.
# EXAMPLES
# This example prints the 'ID' and 'protein names' field of the proteins
# retrieved from UniProt, searching 'russula'.
use WWW::UniProt;
@result = WWW::UniProt::search 'russula', {columns => ['id', 'protein names']};
print "ID: ${$_}{'id'}, Protein names: ${$_}{'protein names'}\n" for (@result);
# AUTHOR
Alfredo Mungo
# LICENSE
This library is free software; you may redistribute it and/or modify it under
the same terms as Perl itself.
# SEE ALSO
[LWP](https://metacpan.org/pod/LWP)