Module MEME

source code

Classes

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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.

MEMEParser
A parser for the text output of the MEME program.

_MEMEScanner
Scanner for MEME output.

_MEMEConsumer
Consumer that can receive events from MEME Scanner.

_MASTConsumer
Consumer that can receive events from _MASTScanner.

MASTParser
Parser for MAST text output.

_MASTScanner
Scanner for MAST text output.

MASTRecord
The class for holding the results from a MAST run.

Functions

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read(handle)
Parses the text output of the MEME program into MEME.Record object.

source code

__read_version(record, handle)

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__read_datafile(record, handle)

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__read_alphabet(record, handle)

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__read_sequence_names(record, handle)

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__read_command(record, handle)

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__create_motif(line)

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__read_motif_name(motif, handle)

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__read_motif_sequences(motif, handle, rv)

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__skip_unused_lines(handle)

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Variables

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StringTypes = (<type 'str'>, <type 'unicode'>)

__package__ = 'Bio.Motif.Parsers'

xml_support = 1

Function Details

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read(handle)

source code

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

Example:

>>> f = open("meme.output.txt")
>>> from Bio.Motif.Parsers import MEME
>>> 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