Package motifs

Parses an output file of motif finding programs.

Currently supported formats (case is ignored):
 - AlignAce:      AlignAce output file format
 - MEME:          MEME output file motif
 - MAST:          MAST output file motif
 - TRANSFAC:      TRANSFAC database file format
 - pfm:           JASPAR-style position-frequency matrix
 - sites:         JASPAR-style sites file
As files in the pfm and sites formats contain only a single motif,
it is easier to use Bio.motifs.read() instead of Bio.motifs.parse()
for those.

For example:

>>> from Bio import motifs
>>> for m in motifs.parse(open("Motif/alignace.out"),"AlignAce"):
...     print m.consensus
TCTACGATTGAG
CTGCAGCTAGCTACGAGTGAG
GTGCTCTAAGCATAGTAGGCG
GCCACTAGCAGAGCAGGGGGC
CGACTCAGAGGTT
CCACGCTAAGAGAGGTGCCGGAG
GCGCGTCGCTGAGCA
GTCCATCGCAAAGCGTGGGGC
GGGATCAGAGGGCCG
TGGAGGCGGGG
GACCAGAGCTTCGCATGGGGG
GGCGTGCGTG
GCTGGTTGCTGTTCATTAGG
GCCGGCGGCAGCTAAAAGGG
GAGGCCGGGGAT
CGACTCGTGCTTAGAAGG

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

This supports the same formats as Bio.motifs.parse(), but
only for files containing exactly one motif.  For example,
reading a JASPAR-style pfm file:

>>> from Bio import motifs
>>> m = motifs.read(open("motifs/SRF.pfm"), "pfm")
>>> m.consensus
Seq('GCCCATATATGG', IUPACUnambiguousDNA())

Or a single-motif MEME file,

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

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

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

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

>>> from Bio import motifs
>>> record = motifs.parse(open("motifs/alignace.out"),"alignace")
>>> motif = record[0]
>>> motif.consensus
Seq('TCTACGATTGAG', IUPACUnambiguousDNA())

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

Returns a string representation of motifs in a given format

Currently supported fromats (case is ignored):
 - pfm : JASPAR Position Frequency Matrix
         [only if len(motifs)==1]
 - transfac : TRANSFAC like files