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A Python interface to query and access different versions of JASPAR database

Project description

pyJASPAR

A Python interface to query and access JASPAR motifs from different releases of JASPAR database using BioPython and sqlite3.

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pyJASPAR provides access to JASPAR database releases including:

Documentation

A detailed documentation is available in different formats: HTML | PDF | ePUB

Installation

Quick installation using conda

pyJASPAR is available on Bioconda for installation via conda.

conda install -c bioconda pyjaspar

Install using pip

pyJASPAR is also available on PyPi for installation via pip.

pip install pyjaspar

pyJASPAR uses BioPython and it supports python 3.x.

Install pyjaspar from source

You can install a development version by using git from GitHub.

Install development version from GitHub

If you have git installed, use this:

git clone https://github.com/asntech/pyjaspar.git
cd pyjaspar
python setup.py sdist install

How to use pyJASPAR?

Once you have installed pyjaspar, you can type:

>>> from pyjaspar import jaspardb

#get the JASPAR2020 release object
>>> jdb_obj = jaspardb(release='JASPAR2020')

#Fetch motif by ID
>>> motif = jdb_obj.fetch_motif_by_id('MA0095')
>>> print(motif)
TF name YY1
Matrix ID   MA0095.2
Collection  CORE
TF class    C2H2 zinc finger factors
TF family   More than 3 adjacent zinc finger factors
Species 9606
Taxonomic group vertebrates
Accession   ['P25490']
Data type used  ChIP-seq
Medline 18950698
PAZAR ID    TF0000069
Matrix:
        0      1      2      3      4      5      6      7      8      9     10     11
A: 1126.00 6975.00 6741.00 2506.00 7171.00   0.00  11.00  13.00 812.00 867.00 899.00 1332.00
C: 4583.00   0.00  99.00 1117.00   0.00  12.00   0.00   0.00 5637.00 1681.00 875.00 4568.00
G: 801.00 181.00 268.00 3282.00   0.00   0.00 7160.00 7158.00  38.00 2765.00 4655.00 391.00
T: 661.00  15.00  63.00 266.00   0.00 7159.00   0.00   0.00 684.00 1858.00 742.00 880.00

## get CORE vertebrates collection of motifs
>>> motifs = jdb_obj.fetch_motifs(
    collection = 'CORE',
    tax_group = ['vertebrates']
    )
>>> for motif in motifs:
        print(motif.matrix_id)
        print(motif.counts)
        # do something with the motif

Get available release

>>> print(jdb_obj.get_releases())
Available JASPAR releases are: ['JASPAR2020', 'JASPAR2018', 'JASPAR2016', 'JASPAR2014']

Project details


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Source Distribution

pyjaspar-1.0.0.tar.gz (37.5 MB view hashes)

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