def parse(handle, format, strict=True):
"""Parse an output file from a motif finding program.
Currently supported formats (case is ignored):
- AlignAce: AlignAce output file format
- ClusterBuster: Cluster Buster position frequency matrix format
- XMS: XMS matrix format
- MEME: MEME output file motif
- MINIMAL: MINIMAL MEME output file motif
- MAST: MAST output file motif
- TRANSFAC: TRANSFAC database file format
- pfm-four-columns: Generic position-frequency matrix format with four columns. (cisbp, homer, hocomoco, neph, tiffin)
- pfm-four-rows: Generic position-frequency matrix format with four row. (scertf, yetfasco, hdpi, idmmpmm, flyfactor survey)
- pfm: JASPAR-style position-frequency matrix
- jaspar: JASPAR-style multiple PFM format
- 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
>>> with open("motifs/alignace.out") as handle:
... for m in motifs.parse(handle, "AlignAce"):
... print(m.consensus)
...
TCTACGATTGAG
CTGCACCTAGCTACGAGTGAG
GTGCCCTAAGCATACTAGGCG
GCCACTAGCAGAGCAGGGGGC
CGACTCAGAGGTT
CCACGCTAAGAGAAGTGCCGGAG
GCACGTCCCTGAGCA
GTCCATCGCAAAGCGTGGGGC
GAGATCAGAGGGCCG
TGGACGCGGGG
GACCAGAGCCTCGCATGGGGG
AGCGCGCGTG
GCCGGTTGCTGTTCATTAGG
ACCGACGGCAGCTAAAAGGG
GACGCCGGGGAT
CGACTCGCGCTTACAAGG
If strict is True (default), the parser will raise a ValueError if the
file contents does not strictly comply with the specified file format.
"""
format = format.lower()
if format == "alignace":
from Bio.motifs import alignace
return alignace.read(handle)
elif format == "meme":
from Bio.motifs import meme
return meme.read(handle)
elif format == "minimal":
from Bio.motifs import minimal
return minimal.read(handle)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
return clusterbuster.read(handle)
elif format in ("pfm-four-columns", "pfm-four-rows"):
from Bio.motifs import pfm
return pfm.read(handle, format)
elif format == "xms":
from Bio.motifs import xms
return xms.read(handle)
elif format == "mast":
from Bio.motifs import mast
return mast.read(handle)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.read(handle, strict)
elif format in ("pfm", "sites", "jaspar"):
from Bio.motifs import jaspar
return jaspar.read(handle, format)
else:
raise ValueError("Unknown format %s" % format)
def parse(handle, format, strict=True):
"""Parse an output file from a motif finding program.
Currently supported formats (case is ignored):
- AlignAce: AlignAce output file format
- ClusterBuster: Cluster Buster position frequency matrix format
- XMS: XMS matrix format
- MEME: MEME output file motif
- MINIMAL: MINIMAL MEME output file motif
- MAST: MAST output file motif
- TRANSFAC: TRANSFAC database file format
- pfm-four-columns: Generic position-frequency matrix format with four columns. (cisbp, homer, hocomoco, neph, tiffin)
- pfm-four-rows: Generic position-frequency matrix format with four row. (scertf, yetfasco, hdpi, idmmpmm, flyfactor survey)
- pfm: JASPAR-style position-frequency matrix
- jaspar: JASPAR-style multiple PFM format
- 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
>>> with open("motifs/alignace.out") as handle:
... for m in motifs.parse(handle, "AlignAce"):
... print(m.consensus)
...
TCTACGATTGAG
CTGCACCTAGCTACGAGTGAG
GTGCCCTAAGCATACTAGGCG
GCCACTAGCAGAGCAGGGGGC
CGACTCAGAGGTT
CCACGCTAAGAGAAGTGCCGGAG
GCACGTCCCTGAGCA
GTCCATCGCAAAGCGTGGGGC
GAGATCAGAGGGCCG
TGGACGCGGGG
GACCAGAGCCTCGCATGGGGG
AGCGCGCGTG
GCCGGTTGCTGTTCATTAGG
ACCGACGGCAGCTAAAAGGG
GACGCCGGGGAT
CGACTCGCGCTTACAAGG
If strict is True (default), the parser will raise a ValueError if the
file contents does not strictly comply with the specified file format.
"""
format = format.lower()
if format == "alignace":
from Bio.motifs import alignace
return alignace.read(handle)
elif format == "meme":
from Bio.motifs import meme
return meme.read(handle)
elif format == "minimal":
from Bio.motifs import minimal
return minimal.read(handle)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
return clusterbuster.read(handle)
elif format in ('pfm-four-columns', 'pfm-four-rows'):
from Bio.motifs import pfm
return pfm.read(handle, format)
elif format == "xms":
from Bio.motifs import xms
return xms.read(handle)
elif format == "mast":
from Bio.motifs import mast
return mast.read(handle)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.read(handle, strict)
elif format in ('pfm', 'sites', 'jaspar'):
from Bio.motifs import jaspar
return jaspar.read(handle, format)
else:
raise ValueError("Unknown format %s" % format)