Package Bio :: Package motifs :: Package jaspar :: Module db
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Module db

source code

Provides read access to a JASPAR5 formatted database.

This modules requires MySQLdb to be installed.

Example, substitute the your database credentials as appropriate:

>>> from Bio.motifs.jaspar.db import JASPAR5
>>>
>>> JASPAR_DB_HOST = "hostname.example.org"
>>> JASPAR_DB_NAME = "JASPAR_2013"
>>> JASPAR_DB_USER = "guest"
>>> JASPAR_DB_PASS = "guest"
>>>
>>> DFLT_COLLECTION = 'CORE'
>>> jdb = JASPAR5(
...     host=JASPAR_DB_HOST,
...     name=JASPAR_DB_NAME,
...     user=JASPAR_DB_USER,
...     password=JASPAR_DB_PASS
... )
>>>
>>>
>>> ets1 = jdb.fetch_motif_by_id('MA0098')
>>> print(ets1)
TF name ETS1
Matrix ID   MA0098.1
Collection  CORE
TF class    Winged Helix-Turn-Helix
TF family   Ets
Species 9606
Taxonomic group vertebrates
Accession   ['CAG47050']
Data type used  SELEX
Medline 1542566
PAZAR ID    TF0000070
Comments    -
Matrix:
        0      1      2      3      4      5
A:   4.00  17.00   0.00   0.00   0.00   5.00
C:  16.00   0.00   1.00  39.00  39.00   3.00
G:   4.00   0.00   0.00   1.00   0.00  17.00
T:  16.00  23.00  39.00   0.00   1.00  15.00
>>>
>>> motifs = jdb.fetch_motifs(
...     collection = 'CORE',
...     tax_group = ['vertebrates', 'insects'],
...     tf_class = 'Winged Helix-Turn-Helix',
...     tf_family = ['Forkhead', 'Ets'],
...     min_ic = 12
... )
>>>
>>> for motif in motifs:
...     pass # do something with the motif
Classes [hide private]
  JASPAR5
Class representing a JASPAR5 DB.
Variables [hide private]
  JASPAR_DFLT_COLLECTION = 'CORE'