def denovo_consensus(self):
inpute_fasta_name = self.args.input
rid,s =best_template_by_blasr(inpute_fasta_name)
prefix = self.args.out_file_name.split(".")
if len(prefix) > 1:
prefix = ".".join(prefix[:-1])
else:
prefix = ".".join(prefix)
full_prefix = os.path.join(self.args.out_dir_name, prefix)
with open("%s_ref.fa" % full_prefix, "w") as f:
print >>f ,">%s_ref" % self.args.consensus_seq_name
print >>f, s
hp_corr = False if self.args.disable_hp_corr else True
generate_haplotype_consensus(inpute_fasta_name, "%s_ref.fa" % full_prefix, full_prefix, self.args.consensus_seq_name,
hpFix = hp_corr,
min_iteration = int(self.args.niter),
max_num_reads = self.args.max_num_reads,
entropy_th = self.args.entropy_th)
def denovoConsensus(self):
prefix = self.args.out_file_name.split(".")
input_fasta_name = self.args.input
rid,s =best_template_by_blasr(input_fasta_name)
if len(prefix) > 1:
prefix = ".".join(prefix[:-1])
else:
prefix = ".".join(prefix)
full_prefix = os.path.join(self.args.out_dir_name, prefix)
with open("%s_ref.fa" % full_prefix, "w") as f:
print >>f ,">%s_ref" % self.args.consensus_seq_name
print >>f, s
hp_corr = False if self.args.disable_hp_corr else True
generate_consensus(input_fasta_name, "%s_ref.fa" % full_prefix, full_prefix, self.args.consensus_seq_name,
hp_corr, int(self.args.niter),
int(self.args.max_num_reads),
float(self.args.entropy_th),
self.args.dump_dag_info,
int(self.args.min_cov))