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

Project description


A serverless interface to Biopython to query and access JASPAR motifs from different releases of JASPAR database using sqlite3. Documentation Status
pyJASPAR provides access to JASPAR database releases including:


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


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
cd pyjaspar
python 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(

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

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

Find available releases

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

Project details

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Source Distribution

pyjaspar-1.5.0.tar.gz (37.5 MB view hashes)

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