Package Bio :: Package motifs :: Module meme
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Module meme

source code

Classes [hide private]
  Motif
A subclass of Motif used in parsing MEME (and MAST) output.
  Instance
A class describing the instances of a MEME motif, and the data thereof.
  Record
A class for holding the results of a MEME run.
Functions [hide private]
 
read(handle)
Parses the text output of the MEME program into a meme.Record object.
source code
 
__read_version(record, handle) source code
 
__read_datafile(record, handle) source code
 
__read_alphabet(record, handle) source code
 
__read_sequences(record, handle) source code
 
__read_command(record, handle) source code
 
__read_motif_statistics(line) source code
 
__read_motif_name(handle) source code
 
__read_motif_sequences(handle, motif_name, alphabet, length, revcomp) source code
 
__skip_unused_lines(handle) source code
Variables [hide private]
  __package__ = 'Bio.motifs'
Function Details [hide private]

read(handle)

source code 
Parses the text output of the MEME program into a meme.Record object.

Example:

>>> from Bio.motifs import meme
>>> with open("meme.output.txt") as f:
...     record = meme.read(f)
>>> for motif in record:
...     for instance in motif.instances:
...         print(instance.motif_name, instance.sequence_name, instance.strand, instance.pvalue)