def write(motifs, format):
"""Return a string representation of motifs in the given format.
Currently supported formats (case is ignored):
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR simple single Position Frequency Matrix
- jaspar : JASPAR multiple PFM format
- transfac : TRANSFAC like files
"""
format = format.lower()
if format in ("pfm", "jaspar"):
from Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.write(motifs)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def __format__(self, format_spec):
"""Return a string representation of the Motif in the given format.
Currently supported formats:
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR single Position Frequency Matrix
- jaspar : JASPAR multiple Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format_spec in ("pfm", "jaspar"):
from Bio.motifs import jaspar
motifs = [self]
return jaspar.write(motifs, format_spec)
elif format_spec == "transfac":
from Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
elif format_spec == "clusterbuster":
from Bio.motifs import clusterbuster
motifs = [self]
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format_spec)
def write(motifs, format):
"""Return a string representation of motifs in the given format.
Currently supported formats (case is ignored):
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR simple single Position Frequency Matrix
- jaspar : JASPAR multiple PFM format
- transfac : TRANSFAC like files
"""
format = format.lower()
if format in ("pfm", "jaspar"):
from Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.write(motifs)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def format(self, format):
"""Return a string representation of the Motif in the given format.
Currently supported fromats:
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR single Position Frequency Matrix
- jaspar : JASPAR multiple Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format in ('pfm', 'jaspar'):
from Bio.motifs import jaspar
motifs = [self]
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
motifs = [self]
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
