Package Motif

Parses an output file of motif finding programs.

Currently supported formats:
 - AlignAce
 - MEME

You can also use single-motif formats, although the Bio.Motif.read()
function is simpler to use in this situation.
 - jaspar-pfm
 - jaspar-sites

For example:

>>> from Bio import Motif
>>> for motif in Motif.parse(open("Motif/alignace.out"),"AlignAce"):
...     print motif.consensus()
TCTACGATTGAG
CTGCACCTAGCTACGAGTGAG
GTGCCCTAAGCATACTAGGCG
GCCACTAGCAGAGCAGGGGGC
CGACTCAGAGGTT
CCACGCTAAGAGAAGTGCCGGAG
GCACGTCCCTGAGCA
GTCCATCGCAAAGCGTGGGGC
GAGATCAGAGGGCCG
TGGACGCGGGG
GACCAGAGCCTCGCATGGGGG
AGCGCGCGTG
GCCGGTTGCTGTTCATTAGG
ACCGACGGCAGCTAAAAGGG
GACGCCGGGGAT
CGACTCGCGCTTACAAGG

Reads a motif from a handle using a specified file-format.

This supports the same formats as Bio.Motif.parse(), but
only for files containing exactly one record.  For example,
reading a pfm file:

>>> from Bio import Motif
>>> motif = Motif.read(open("Motif/SRF.pfm"),"jaspar-pfm")
>>> motif.consensus()
Seq('GCCCATATATGG', IUPACUnambiguousDNA())

Or a single-motif MEME file,

>>> from Bio import Motif
>>> motif =  Motif.read(open("Motif/meme.out"),"MEME")
>>> motif.consensus()
Seq('CTCAATCGTA', IUPACUnambiguousDNA())

If the handle contains no records, or more than one record,
an exception is raised:

>>> from Bio import Motif
>>> motif = Motif.read(open("Motif/alignace.out"),"AlignAce")
Traceback (most recent call last):
    ...
ValueError: More than one motif found in handle

If however you want the first record from a file containing
multiple records this function would raise an exception (as
shown in the example above).  Instead use:

>>> from Bio import Motif
>>> motif = Motif.parse(open("Motif/alignace.out"),"AlignAce").next()
>>> motif.consensus()
Seq('TCTACGATTGAG', IUPACUnambiguousDNA())

Use the Bio.Motif.parse(handle, format) function if you want
to read multiple records from the handle.