I try to create some motif logos. Now I follow biopython example and write script like following, it works well when dataset is small, but fails for large dataset. And there are several web tools can create motif logo, but, still, they has input limitation. Any suggestions?
for motif in tot: m = Motif.Motif(alphabet=IUPAC.unambiguous_dna) for i in tot[motif]: m.add_instance(Seq(i,m.alphabet)) print >>fao, m.format("transfac") #PWM pic=motif+".png" m.weblogo(pic) #logo
"tot" is a dictionary, "motif" are keys of "tot", which are different motif(such as "TANNTA") I am looking for, and key values are list, which have exact motif sequence as elements (["TATTTA","TAGGTA",.....]).