def DrerioRange(chromoname, begin, end): print "D.rerio %s %d %d" % (chromoname, begin, end) b,e = map(int, [begin, end]) fragrest = fetchREST('Danio rerio', chromoname, b, e) fragensembl = str(ensembl.Binomial('danio').chromosome(chromoname)[b:e+1]) util.asFASTA(fragrest, open('D.rerio%srest.fas' % chromoname, 'w'), title='D.rerio chromosome %s %d to %d from REST'%(chromoname, b, e)) util.asFASTA(fragensembl, open('D.rerio%sensembl.fas' % chromoname, 'w'), title='D.rerio chromosome %s %d to %d from Ensembl'%(chromoname, b, e)) assert fragrest == fragensembl
def asFASTA(self, out, linelength=79): """To the file object *out*, write the seuqnce in FASTA format. Lines will be limited to *linelength* characters (each line will have an additional newline). """ return util.asFASTA(self[:], out, title=repr(self), linelength=linelength)