def check(self):
# Prepare #
self.clean()
if self.verbose: print Color.l_ylw + "----> Subsampling down to %i" % (self.downto,) + Color.end
sys.stdout.flush()
self.fasta.subsample(self.downto, self.subsampled.path)
# Cluster #
if self.verbose: print Color.l_ylw + "----> Running derep_prefix on %s" % (self.subsampled.path,) + Color.end
sys.stdout.flush()
command = ("-derep_prefix", self.subsampled.path, "-output", self.derep_cluster.path, "-sizeout")
sh.usearch6(command)
# Detect #
if self.verbose: print Color.l_ylw + "----> Running uchime_ref on %s" % (self.derep_cluster.path,) + Color.end
sys.stdout.flush()
command = ("-uchime_ref", self.derep_cluster.path, "-db", chimera_ref_path, "-strand", "plus",
"-chimeras", self.positive.path, "-nonchimeras", self.negative.path)
sh.usearch6(command)
def check(self):
# Prepare #
self.clean()
if self.verbose: print Color.l_ylw + "----> Subsampling down to %i" % (self.downto,) + Color.end
sys.stdout.flush()
self.fasta.subsample(self.downto, self.subsampled.path)
# Cluster #
if self.verbose: print Color.l_ylw + "----> Running derep_prefix on %s" % (self.subsampled.path,) + Color.end
sys.stdout.flush()
command = ("-derep_prefix", self.subsampled.path, "-output", self.derep_cluster.path, "-sizeout")
sh.usearch6(command)
# Detect #
if self.verbose: print Color.l_ylw + "----> Running uchime_ref on %s" % (self.derep_cluster.path,) + Color.end
sys.stdout.flush()
command = ("-uchime_ref", self.derep_cluster.path, "-db", chimera_ref_path, "-strand", "plus",
"-chimeras", self.positive.path, "-nonchimeras", self.negative.path)
sh.usearch6(command)
def check(self):
# Prepare #
self.clean()
if self.verbose: print Color.l_ylw + "----> Subsampling down to %i" % (self.downto,) + Color.end
sys.stdout.flush()
self.fasta.subsample(self.downto, self.subsampled.path)
# Cluster #
if self.verbose: print Color.l_ylw + "----> Running cluster_fast on %s" % (self.subsampled.path,) + Color.end
sys.stdout.flush()
command = ("-cluster_fast", self.subsampled.path, "-id", '0.99',
"-consout", self.cluster_99.path, "-sizeout")
sh.usearch6(command)
# Detect #
if self.verbose: print Color.l_ylw + "----> Running uchime_denovo on %s" % (self.cluster_99.path,) + Color.end
sys.stdout.flush()
command = ("-uchime_denovo", self.cluster_99.path,
"-chimeras", self.positive.path, "-nonchimeras", self.negative.path)
sh.usearch6(command)
def check(self):
# Prepare #
self.clean()
if self.verbose: print Color.l_ylw + "----> Subsampling down to %i" % (self.downto,) + Color.end
sys.stdout.flush()
self.fasta.subsample(self.downto, self.subsampled.path)
# Cluster #
if self.verbose: print Color.l_ylw + "----> Running cluster_fast on %s" % (self.subsampled.path,) + Color.end
sys.stdout.flush()
command = ("-cluster_fast", self.subsampled.path, "-id", '0.99',
"-consout", self.cluster_99.path, "-sizeout")
sh.usearch6(command)
# Detect #
if self.verbose: print Color.l_ylw + "----> Running uchime_denovo on %s" % (self.cluster_99.path,) + Color.end
sys.stdout.flush()
command = ("-uchime_denovo", self.cluster_99.path,
"-chimeras", self.positive.path, "-nonchimeras", self.negative.path)
sh.usearch6(command)
