def make_alf_dirs_(self): """ DEPRECATED """ alf_dirs = {} for k in range(self.num_classes): dirname = fileIO.join_path(self.tmpdir, "class{0:0>1}".format(k + 1)) alf_dirs[k + 1] = errors.directorymake(dirname) self.alf_dirs = alf_dirs
def make_alf_dirs_(self): """ DEPRECATED """ alf_dirs = {} for k in range(self.num_classes): dirname = fileIO.join_path(self.tmpdir, 'class{0:0>1}'.format(k + 1)) alf_dirs[k + 1] = errors.directorymake(dirname) self.alf_dirs = alf_dirs
def write(self): if hasattr(self, 'result'): errors.directorymake(self.outdir) errors.directorymake(fileIO.join_path(self.outdir, 'base_class_trees')) errors.directorymake(fileIO.join_path(self.outdir, 'gene_trees')) for rec in self.result: filename = fileIO.join_path(self.outdir, rec.name) + '.phy' rec.write_phylip(filename, interleaved=True) for i in range(self.num_classes): tree = self.class_trees[i+1] name = 'base_tree_class{0:0>{1}}.nwk'.format(i+1, len(str(self.num_classes))) filename = fileIO.join_path(self.outdir, 'base_class_trees', name) tree.write_to_file(filename) for i, tree in enumerate(self.gene_trees, start=1): filename = fileIO.join_path(self.outdir, 'gene_trees', tree.name+'.nwk') tree.write_to_file(filename) self.master_tree.write_to_file(fileIO.join_path(self.outdir, 'master_tree.nwk')) filename = fileIO.join_path(self.outdir, 'true_partition.txt') with open(filename, 'w') as partition_file: partition_file.write(repr(self.true_partition))
def write(self): if hasattr(self, 'result'): errors.directorymake(self.outdir) errors.directorymake( fileIO.join_path(self.outdir, 'base_class_trees')) errors.directorymake(fileIO.join_path(self.outdir, 'gene_trees')) for rec in self.result: filename = fileIO.join_path(self.outdir, rec.name) + '.phy' rec.write_phylip(filename, interleaved=True) for i in range(self.num_classes): tree = self.class_trees[i + 1] name = 'base_tree_class{0:0>{1}}.nwk'.format( i + 1, len(str(self.num_classes))) filename = fileIO.join_path(self.outdir, 'base_class_trees', name) tree.write_to_file(filename) for i, tree in enumerate(self.gene_trees, start=1): filename = fileIO.join_path(self.outdir, 'gene_trees', tree.name + '.nwk') tree.write_to_file(filename) self.master_tree.write_to_file( fileIO.join_path(self.outdir, 'master_tree.nwk')) filename = fileIO.join_path(self.outdir, 'true_partition.txt') with open(filename, 'w') as partition_file: partition_file.write(repr(self.true_partition))
def write(self): if hasattr(self, "result"): errors.directorymake(self.outdir) errors.directorymake(fileIO.join_path(self.outdir, "base_class_trees")) errors.directorymake(fileIO.join_path(self.outdir, "gene_trees")) for rec in self.result: filename = fileIO.join_path(self.outdir, rec.name) + ".phy" rec.write_phylip(filename, interleaved=True) for i in range(self.num_classes): tree = self.class_trees[i + 1] name = "base_tree_class{0:0>{1}}.nwk".format(i + 1, len(str(self.num_classes))) filename = fileIO.join_path(self.outdir, "base_class_trees", name) tree.write_to_file(filename) for i, tree in enumerate(self.gene_trees, start=1): filename = fileIO.join_path(self.outdir, "gene_trees", tree.name + ".nwk") tree.write_to_file(filename) self.master_tree.write_to_file(fileIO.join_path(self.outdir, "master_tree.nwk")) filename = fileIO.join_path(self.outdir, "true_partition.txt") with open(filename, "w") as partition_file: partition_file.write(repr(self.true_partition))
def make_alf_dirs(self): alf_dirs = {} for i, g in enumerate(self.gene_trees, start=1): dirname = fileIO.join_path(self.tmpdir, g.name) alf_dirs[i] = errors.directorymake(dirname) self.alf_dirs = alf_dirs