Bio.motifs.minimal module

Module for the support of MEME minimal motif format.

Bio.motifs.minimal.read(handle)

Parse the text output of the MEME program into a meme.Record object.

Examples

>>> from Bio.motifs import minimal
>>> with open("motifs/meme.out") as f:
...     record = minimal.read(f)
...
>>> for motif in record:
...     print(motif.name, motif.evalue)
...
1 1.1e-22

You can access individual motifs in the record by their index or find a motif by its name:

>>> from Bio import motifs
>>> with open("motifs/minimal_test.meme") as f:
...     record = motifs.parse(f, 'minimal')
...
>>> motif = record[0]
>>> print(motif.name)
KRP
>>> motif = record['IFXA']
>>> print(motif.name)
IFXA

This function wont retrieve instances, as there are none in minimal meme format.

class Bio.motifs.minimal.Record

Bases: list

Class for holding the results of a minimal MEME run.

__init__(self)

Initialize record class values.

__getitem__(self, key)

Return the motif of index key.