Package Bio :: Package Motif :: Package Parsers :: Module MEME
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Module MEME

source code

Classes [hide private]
  MEMEMotif
A subclass of Motif used in parsing MEME (and MAST) output.
  MEMEInstance
A class describing the instances of a MEME motif, and the data thereof.
  MEMERecord
A class for holding the results of a MEME run.
Functions [hide private]
 
read(handle)
Parses the text output of the MEME program into MEME.Record object.
source code
 
__read_version(record, handle) source code
 
__read_datafile(record, handle) source code
 
__read_alphabet(record, handle) source code
 
__read_sequence_names(record, handle) source code
 
__read_command(record, handle) source code
 
__create_motif(line) source code
 
__read_motif_name(motif, handle) source code
 
__read_motif_sequences(motif, handle, rv) source code
 
__skip_unused_lines(handle) source code
Variables [hide private]
  __package__ = 'Bio.Motif.Parsers'
Function Details [hide private]

read(handle)

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

Example:

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