def label(self) :
self.seqdb = self.__read_fasta(self.options['cluster-fasta'])
blast_fname = self.options['cluster-fasta']
# if we are only going to label the clusters without labels
# then we need to find the names of those clusters and write a
# fasta file containing only those sequences
if self.options['label-missing'] :
tmp = []
biom = json.load(open(self.options['cluster-biom']))
for r in biom['rows'] :
if r['metadata']['label'] in ("", "unknown", "error", "cannot label (matches multiple domains!)") :
tmp.append(r['id'])
if len(tmp) == 0 :
self.log.error("there are no missing labels")
exit(1)
self.log.info("%d clusters missing labels" % len(tmp))
blast_fname = self.__fasta(join(self.options['outdir'], 'missing.fasta'), tmp)
print "getting OTU names (this may take a while)..."
otu_names = BlastN(self.options['verbose']).get_names(blast_fname, self.options['labels'], self.options['labels-similarity'], self.options['labels_db'])
# rework the biom
biom = BiomFile()
biom.change_otu_names(self.options['cluster-biom'], otu_names)
self.log.info("written %s" % self.options['cluster-biom'])
# get the rest of the names and rewrite fasta
otu_names = biom.get_label_mapping(self.options['cluster-biom'])
self.__fasta(self.options['cluster-fasta'], self.seqdb.keys(), names=otu_names)
return 0
def __biom(self, filename, samples, clustering, cluster_names) :
centroids = clustering.centroids()
all_keys = clustering.all()
output_clusters = clustering.clusters
output_samples = [ s for s in samples if s.contains(all_keys) ]
output_otus = [ ("seance" + str(k), cluster_names.get("seance" + str(k), "unknown")) for k in centroids ]
#self.log.info("%d / %d samples have at least one sequence used in clustering" % \
# (len(output_samples), len(samples)))
b = BiomFile()
b.set_samples(output_samples)
b.set_otus(output_otus)
for sind,sample in enumerate(output_samples) :
for cind,cluster in enumerate(output_clusters) :
count = 0
for read in cluster :
if read in sample :
count += sample.seqcounts[read]
b.add_quantity(cind, sind, count)
b.write_to(filename)
self.log.info("written %s" % filename)
def showlabels(self) :
delim = self.options['delimiter']
#biom = json.load(open(self.options['cluster-biom']))
#
#for r in biom['rows'] :
# print delim.join([r['id'], r['metadata']['label']])
biom = BiomFile()
labels = biom.get_label_mapping(self.options['cluster-biom'])
for x in labels.iteritems() :
print delim.join(x)
return 0
