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

source code

Submodules [hide private]

Classes [hide private]
  Motif
A subclass of Bio.motifs.Motif used to represent a JASPAR profile with additional metadata information if available.
  Record
Represents 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)
Returns the representation of the motifs in "pfm" or "jaspar" format...
source code
 
_read_pfm(handle)
Reads the motif from a JASPAR .pfm file
source code
 
_read_sites(handle)
Reads 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 base ID and version number, e.g.
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.
Call the appropriate routine based on the format passed.

write(motifs, format)

source code 
Returns the representation of the motifs in "pfm" or "jaspar" format
    

_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 ]

split_jaspar_id(id)

source code 

Utility function to split a JASPAR matrix ID into its component base ID
and version number, e.g. 'MA0047.2' is returned as ('MA0047', 2).