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)