A serverless interface to Biopython to access different versions of JASPAR database
Project description
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:
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
Find available releases
>>> print(jdb_obj.get_releases())
Available JASPAR releases are: ['JASPAR2020', 'JASPAR2018', 'JASPAR2016', 'JASPAR2014']
Project details
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