def getMotifGff(self):
"""Get a GFF with the best motifs for all sequences"""
gff_dict = self.findMotifs()
gff = []
for motif in gff_dict.values():
gff.extend(motif)
bestfile = GffFile()
bestfile.gff = gff
gfffilename = self.tempFile("gff", bestfile.getFormattedGff())
return gfffilename
def findMotifs(self):
"""Fill a best-results dictionary and return it"""
if len(self.seqs) == 0 and self.fastafilename is None:
raise ValueError("Please add some sequences to find motifs in")
if self.bgfilename is None:
self.bgfilename = self.tempFile("bg", "")
self.createBackground(self.fastafilename, self.bgfilename)
if self.immfilename is None:
self.sampleFiles()
gffoutfilename = self.scanFiles(0.9999)
gff = GffFile()
gff.read(gffoutfilename, "")
best_dict = gff.getAllMotifsAllGenes()
return best_dict