Package Bio :: Package motifs :: Package jaspar
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Package jaspar

source code

JASPAR2014 module. 

Submodules [hide private]

Classes [hide private]
  Motif
A subclass of Bio.motifs.Motif used to represent a JASPAR profile.
  Record
Represent a list of jaspar motifs.
Functions [hide private]
 
read(handle, format)
Read motif(s) from a file in one of several different JASPAR formats.
source code
 
write(motifs, format)
Return the representation of motifs in "pfm" or "jaspar" format.
source code
 
_read_pfm(handle)
Read the motif from a JASPAR .pfm file.
source code
 
_read_sites(handle)
Read the motif from JASPAR .sites file.
source code
 
_read_jaspar(handle)
Read motifs from a JASPAR formatted file.
source code
 
calculate_pseudocounts(motif) source code
 
split_jaspar_id(id)
Utility function to split a JASPAR matrix ID into its component.
source code
Variables [hide private]
  __package__ = 'Bio.motifs.jaspar'
Function Details [hide private]

read(handle, format)

source code 

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.

_read_jaspar(handle)

source code 

Read motifs from a JASPAR formatted file.

Format is one or more records of the form, e.g.:
>MA0001.1 AGL3
A  [ 0  3 79 40 66 48 65 11 65  0 ]
C  [94 75  4  3  1  2  5  2  3  3 ]
G  [ 1  0  3  4  1  0  5  3 28 88 ]
T  [ 2 19 11 50 29 47 22 81  1  6 ]

or
>MA0001.1 AGL3
0  3 79 40 66 48 65 11 65  0
4 75  4  3  1  2  5  2  3  3
1  0  3  4  1  0  5  3 28 88
2 19 11 50 29 47 22 81  1  6

split_jaspar_id(id)

source code 

Utility function to split a JASPAR matrix ID into its component.

Components are base ID and version number, e.g. 'MA0047.2' is returned as
('MA0047', 2).