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.
- 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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pyjaspar-1.0.0.tar.gz
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