pyjaspar 4.0.0

pyJASPAR

A Pythonic interface to JASPAR transcription factor motifs

pyJASPAR uses Biopython and SQLite3 to provide a serverless interface to JASPAR database to query and access TF motif profiles across various releases of JASPAR.

pyJASPAR provides access to the following releases of JASPAR database: JASPAR2026, JASPAR2024, JASPAR2022, 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

Note: The JASPAR2026 release is available for peer-review purpose via GitHub only. It will be made public after the official release of JASPAR2026 database.

conda install -c bioconda pyjaspar

pip install pyjaspar

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

#Create the JASPAR2026 release object
>>> jdb_obj = jaspardb(release='JASPAR2026')

#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_motifs_by_name('KFL4')
>>> print(len(motifs))
1

# Get a dictionary of frequency count matrics
>>> print(motifs[0].counts)
{'A': [2465.0, 2105.0, 7021.0, 1173.0, 45602.0, 852.0, 1617.0, 1202.0],
'C': [49209.0, 47865.0, 45405.0, 52875.0, 161.0, 52366.0, 51112.0, 51045.0],
'G': [1583.0, 1214.0, 1422.0, 793.0, 6598.0, 1470.0, 1870.0, 1005.0],
'T': [2560.0, 4633.0, 1969.0, 976.0, 3456.0, 1129.0, 1218.0, 2565.0]}

#Get CORE vertebrates non-redundent collection
>>> motifs = jdb_obj.fetch_motifs(
        collection = ['CORE'],
        tax_group = ['Vertebrates'],
        all_versions = False)
>>> print(len(motifs))
1019
## 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

>>> print(jdb_obj.get_releases())
['JASPAR2026', 'JASPAR2024','JASPAR2022','JASPAR2020', 'JASPAR2018', 'JASPAR2016', 'JASPAR2014']

@software{aziz_khan_2021_4509415,
  author       = {Aziz Khan},
  title        = {{pyJASPAR: a Pythonic interface to JASPAR transcription factor motifs}},
  month        = feb,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {v4.0.0},
  doi          = {10.5281/zenodo.4485856},
  url          = {https://doi.org/10.5281/zenodo.4485856}
}