Bio.motifs.jaspar package
Submodules
Module contents
JASPAR2014 module.
- class Bio.motifs.jaspar.Motif(matrix_id, name, alphabet='ACGT', alignment=None, counts=None, collection=None, tf_class=None, tf_family=None, species=None, tax_group=None, acc=None, data_type=None, medline=None, pazar_id=None, comment=None)
Bases:
Motif
A subclass of Bio.motifs.Motif used to represent a JASPAR profile.
Additional metadata information are stored if available. The metadata availability depends on the source of the JASPAR motif (a ‘pfm’ format file, a ‘jaspar’ format file or a JASPAR database).
- __init__(matrix_id, name, alphabet='ACGT', alignment=None, counts=None, collection=None, tf_class=None, tf_family=None, species=None, tax_group=None, acc=None, data_type=None, medline=None, pazar_id=None, comment=None)
Construct a JASPAR Motif instance.
- property base_id
Return the JASPAR base matrix ID.
- property version
Return the JASPAR matrix version.
- __str__()
Return a string representation of the JASPAR profile.
We choose to provide only the filled metadata information.
- __hash__()
Return the hash key corresponding to the JASPAR profile.
- Note:
We assume the unicity of matrix IDs
- __eq__(other)
Return True if matrix IDs are the same.
- class Bio.motifs.jaspar.Record
Bases:
list
Represent a list of jaspar motifs.
- Attributes:
version: The JASPAR version used
- __init__()
Initialize the class.
- __str__()
Return a string of all motifs in the Record.
- to_dict()
Return the list of matrices as a dictionary of matrices.
- Bio.motifs.jaspar.read(handle, format)
Read motif(s) from a file in one of several different JASPAR formats.
Return the record of PFM(s). Call the appropriate routine based on the format passed.
- Bio.motifs.jaspar.write(motifs, format)
Return the representation of motifs in “pfm” or “jaspar” format.
- Bio.motifs.jaspar.calculate_pseudocounts(motif)
Calculate pseudocounts.
Computes the root square of the total number of sequences multiplied by the background nucleotide.
- Bio.motifs.jaspar.split_jaspar_id(id)
Split a JASPAR matrix ID into its component.
Components are base ID and version number, e.g. ‘MA0047.2’ is returned as (‘MA0047’, 2).