pyjaspar 1.5.5

A serverless interface to Biopython to access different versions of JASPAR database

pyJASPAR

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

pyJASPAR provides access to JASPAR database releases including:

• JASPAR2020

• JASPAR2018

• JASPAR2016

• JASPAR2014

Note: This is a serverless SQLite wrapper around the Biopython JASPAR module Bio.motifs.jaspar.db which requires JASPAR MySQL database sever connection details.

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 create jaspardb class object:

>>> from pyjaspar import jaspardb

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

#Fetch motif by ID
>>> motif = jdb_obj.fetch_motif_by_id('MA0095.2')
>>> print(motif.name)
YY1

#Fetch motifs by TF name
>>> motifs = jdb_obj.fetch_motif_by_name('CTCF')
>>> print(len(motifs))
2

#Get CORE vertebrates collection
>>> motifs = jdb_obj.fetch_motifs(
    collection = 'CORE',
    tax_group = ['vertebrates']
    )
>>> print(len(motifs))
746
## loop through the motifs list and perform analysis
>>> for motif in motifs:
        pass

Note: Above methods return Bio.motifs.jaspar.Motif object. You can find more details here

Find available releases

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