def phylogeny(self) :
num_sequences = self.__count(self.options['cluster-fasta'])
p = Pagan()
if self.options['subset'] :
self.seqdb = self.__read_fasta(self.options['cluster-fasta'], include=self.options['subset'])
self.options['cluster-fasta'] = self.__fasta(self.options['cluster-fasta'] + '.subset', self.seqdb.keys())
self.log.info("read %d cluster centroids using subset(%s)" % (len(self.seqdb), self.options['subset']))
if not self.options['silva-fasta'] :
self.log.info("aligning %s sequences with PAGAN ..." % (num_sequences))
alignment,tree,xmlfile = p.phylogenetic_alignment(self.options['cluster-fasta'])
else :
self.log.info("aligning %s sequences with PAGAN against SILVA ..." % (num_sequences))
alignment,tree,xmlfile = p.silva_phylogenetic_alignment(self.options['silva-fasta'],
self.options['silva-tree'],
self.options['cluster-fasta'])
os.rename(alignment, self.options['phylogeny-fasta'])
os.rename(tree, self.options['phylogeny-tree'])
os.rename(xmlfile, self.options['phylogeny-xml'])
self.log.info("created %s" % self.options['phylogeny-fasta'])
self.log.info("created %s" % self.options['phylogeny-tree'])
if xmlfile :
self.log.info("created %s" % self.options['phylogeny-xml'])
return 0
