Bio.motifs.jaspar package¶
Submodules¶
Module contents¶
JASPAR2014 module.
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class
Bio.motifs.jaspar.
Motif
(matrix_id, name, alphabet='ACGT', instances=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:
Bio.motifs.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).
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__init__
(self, matrix_id, name, alphabet='ACGT', instances=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.
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property
base_id
¶ Return the JASPAR base matrix ID.
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property
version
¶ Return the JASPAR matrix version.
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__str__
(self)¶ Return a string represention of the JASPAR profile.
We choose to provide only the filled metadata information.
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__hash__
(self)¶ Return the hash key corresponding to the JASPAR profile.
- Note
We assume the unicity of matrix IDs
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__eq__
(self, other)¶ Return True if matrix IDs are the same.
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class
Bio.motifs.jaspar.
Record
¶ Bases:
list
Represent a list of jaspar motifs.
- Attributes:
version: The JASPAR version used
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__init__
(self)¶ Initialize the class.
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__str__
(self)¶ Return a string of all motifs in the Record.
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to_dict
(self)¶ Return the list of matrices as a dictionary of matrices.
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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.
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Bio.motifs.jaspar.
write
(motifs, format)¶ Return the representation of motifs in “pfm” or “jaspar” format.
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Bio.motifs.jaspar.
calculate_pseudocounts
(motif)¶ Calculate pseudocounts.
Computes the root square of the total number of sequences multiplied by the background nucleotide.
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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).