def format(self,format):
"""Returns a string representation of the Motif in a given format
Currently supported fromats:
- pfm : JASPAR Position Frequency Matrix
- transfac : TRANSFAC like files
"""
if format=="pfm":
from Bio.Motif import Jaspar
return Jaspar.write(self)
elif format=="transfac":
from Bio.Motif import TRANSFAC
motifs = [self]
return TRANSFAC.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def write(motifs, format):
"""Returns a string representation of motifs in a given format
Currently supported fromats:
- pfm : JASPAR Position Frequency Matrix
[only if len(motifs)==1]
- transfac : TRANSFAC like files
"""
if format=="pfm":
from Bio.Motif import Jaspar
if len(motifs)!=1:
raise Exception("Only a single motif can be written in the JASPAR Position Frequency Matrix (pfm) format")
motif = motifs[0]
return Jaspar.write(motif)
elif format=="transfac":
from Bio.Motif import TRANSFAC
return TRANSFAC.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
