def __init__(self, samples, name, base_dir=None):
# Save samples #
self.name = name
self.samples, self.children = samples, samples
# Check names are unique #
names = [s.short_name for s in samples if s.used]
assert len(names) == len(set(names))
# Figure out pools #
self.pools = list(set([s.pool for s in self.samples]))
self.pools.sort(key=lambda x: x.id_name)
# Load them #
for p in self.pools:
p.load()
# Dir #
if base_dir: self.base_dir = base_dir
else:
self.base_dir = illumitag.view_dir + "clusters/" + self.name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Runner #
self.runner = ClusterRunner(self)
# FASTA #
self.reads = FASTA(self.p.all_reads_fasta)
# OTU picking #
self.otu_uparse = UparseOTUs(self)
self.otu_uclust = UclustOTUs(self)
self.otu_cdhit = CdhitOTUs(self)
# Reporting #
self.reporter = ClusterReporter(self)
