def _bootstrap(self, rep_num): """Infer tree from bootstrapped multiple sequence alignment. Parameters ---------- replicated_num : int Unique replicate number. cpus : int Number of cpus to use. """ rep_dir = os.path.join(self.output_dir, 'rep_%d' % rep_num) if not os.path.exists(rep_dir): os.makedirs(rep_dir) output_msa = os.path.join(rep_dir, 'bootstrap.afa') bootstrap_alignment(self.msa, output_msa) phylip_msa_file = output_msa.replace('.afa', '.phyx') cmd = 'seqmagick convert %s %s' % (output_msa, phylip_msa_file) os.system(cmd) log_file = os.path.join(rep_dir, 'raxml.log') self.run(phylip_msa_file, self.model, rep_dir, log_file, output_suffix='support') return True
def _producer(self, replicated_num): """Infer tree from bootstrapped multiple sequence alignment. Parameters ---------- replicated_num : int Unique replicate number. """ output_msa = os.path.join( self.replicate_dir, 'bootstrap_msa.r_' + str(replicated_num) + '.fna') if os.path.exists(output_msa) and os.path.getsize(output_msa) > 0: self.logger.warning( 'Skipping {} as it already exists.'.format(output_msa)) return True output_tree = os.path.join( self.replicate_dir, 'bootstrap_tree.r_' + str(replicated_num) + '.tree') fast_tree_output = os.path.join( self.replicate_dir, 'bootstrap_fasttree.r_' + str(replicated_num) + '.out') if os.path.exists( fast_tree_output) and os.path.getsize(fast_tree_output) > 0: self.logger.warning( 'Skipping {} as it already exists.'.format(fast_tree_output)) return True bootstrap_alignment(self.msa, output_msa, frac=self.frac) fast_tree = FastTree(multithreaded=False) cmd = fast_tree.run(output_msa, self.base_type, self.model, self.gamma, output_tree, fast_tree_output) return True
def _producer(self, replicated_num): """Infer tree from bootstrapped multiple sequence alignment. Parameters ---------- replicated_num : int Unique replicate number. """ output_msa = os.path.join( self.replicate_dir, 'bootstrap_msa.r_' + str(replicated_num) + '.fna') bootstrap_alignment(self.msa, output_msa, frac=self.frac) fast_tree = FastTree(multithreaded=False) output_tree = os.path.join( self.replicate_dir, 'bootstrap_tree.r_' + str(replicated_num) + '.tree') fast_tree_output = os.path.join( self.replicate_dir, 'bootstrap_fasttree.r_' + str(replicated_num) + '.out') fast_tree.run(output_msa, self.base_type, self.model, output_tree, fast_tree_output) return True
def _producer(self, replicated_num): """Infer tree from bootstrapped multiple sequence alignment. Parameters ---------- replicated_num : int Unique replicate number. """ output_msa = os.path.join(self.replicate_dir, 'bootstrap_msa.r_' + str(replicated_num) + '.fna') bootstrap_alignment(self.msa, output_msa, frac=self.frac) fast_tree = FastTree(multithreaded=False) output_tree = os.path.join(self.replicate_dir, 'bootstrap_tree.r_' + str(replicated_num) + '.tree') fast_tree_output = os.path.join(self.replicate_dir, 'bootstrap_fasttree.r_' + str(replicated_num) + '.out') fast_tree.run(output_msa, self.base_type, self.model, self.gamma, output_tree, fast_tree_output) return True
def _bootstrap(self, replicated_num): """Infer tree from bootstrapped multiple sequence alignment. Parameters ---------- replicated_num : int Unique replicate number. cpus : int Number of cpus to use. """ output_msa = os.path.join(self.replicate_dir, 'bootstrap.msa.' + str(replicated_num) + '.fna') bootstrap_alignment(self.msa, output_msa) output_tree = os.path.join(self.replicate_dir, 'bootstrap.tree.' + str(replicated_num) + '.tre') fast_tree_output = os.path.join(self.replicate_dir, 'bootstrap.fasttree.' + str(replicated_num) + '.out') self.run(output_msa, self.seq_type, self.model, output_tree, fast_tree_output) return True
def _bootstrap(self, rep_num): """Infer tree from bootstrapped multiple sequence alignment. Parameters ---------- replicated_num : int Unique replicate number. cpus : int Number of cpus to use. """ rep_dir = os.path.join(self.output_dir, 'rep_%d' % rep_num) if not os.path.exists(rep_dir): os.makedirs(rep_dir) output_msa = os.path.join(rep_dir, 'bootstrap.afa') bootstrap_alignment(self.msa, output_msa) output_tree = os.path.join(rep_dir, 'bootstrap.tree') log_file = os.path.join(rep_dir, 'fasttree.log') self.run(output_msa, self.seq_type, self.model, output_tree, log_file) return True