def load_de_numericized_newick_tree(tree_in,before="'",after="'",root=False):
from cogent.core.tree import PhyloNode
from cogent import LoadTree
import os.path
if os.path.isfile(tree_in):
tree = LoadTree(tree_in)
else:
tree = LoadTree(treestring=tree_in)
terminals = tree.getTipNames()
rename_dict = {}
for tip in terminals:
rename_dict[tip] = before + str(tip) + after
tree.reassignNames(rename_dict)
if root:
tree = tree.rootAtMidpoint()
treestring = tree.getNewick(with_distances=True)
return treestring
def main():
# Parse input to get parameters
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
tree_file = opts.input_tree
trait_table_fp = opts.input_trait_table
verbose = opts.verbose
#Handle parameters with more complex defaults
if opts.output_table:
output_table_fp = opts.output_table
else:
output_table_fp = add_to_filename(trait_table_fp,"reformatted")
if opts.output_tree:
output_tree_fp = opts.output_tree
else:
output_tree_fp = add_to_filename(trait_table_fp,"reformatted")
if verbose:
print "Running with options:"
print "%s:%s" %("Tree file",tree_file)
print "%s:%s" %("Trait table",trait_table_fp)
print "%s:%s" %("Output tree",output_tree_fp)
print "%s:%s" %("Output trait table",output_table_fp)
print "%s:%s" %("Add branch length to root",opts.add_branch_length_to_root)
print "%s:%s" %("Convert to NEXUS?",opts.convert_to_nexus)
# Open output files
output_trait_table_file = open(output_table_fp,"w+")
output_tree_file = open(output_tree_fp,"w+")
# Begin reformatting
# TODO: convert parameter candidates to params
#delimiter = "\t"
delimiter = " "
min_branch_length = 0.0001
root_name = "root"
if format_for_bayestraits:
convert_to_nexus = True
convert_to_bifurcating = True
filter_table_by_tree_tips = True
filter_tree_by_table_entries = True
enforce_min_branch_length = True
convert_trait_floats_to_ints = True
#Load inputs
input_tree = LoadTree(tree_file)
trait_table = open(trait_table_fp,"U")
trait_table_lines = trait_table.readlines()
#if opts.verbose:
#print "Tree prior to reformatting:"
#print input_tree.getNewick(with_distances=True)
#print "Tree nodes prior to reformatting:"
#print_node_summary_table(input_tree)
# Remove taxa missing in tree tips
if filter_table_by_tree_tips:
trait_table_lines = filter_table_by_presence_in_tree(input_tree,trait_table_lines,delimiter=delimiter)
#Convert floating point values to ints
if convert_trait_floats_to_ints:
trait_table_lines = convert_trait_values(\
trait_table_lines,conversion_fn = int,delimiter=delimiter)
#Write out results
output_trait_table_file.writelines(trait_table_lines)
trait_table.close()
output_trait_table_file.close()
# Use the reformatted trait table to filter tree
trait_table = open(output_table_fp,"U")
trait_table_lines = trait_table.readlines()
if filter_tree_by_table_entries:
input_tree = filter_tree_tips_by_presence_in_table(input_tree,trait_table_lines,delimiter=delimiter)
# Tree reformatting
if convert_to_bifurcating:
input_tree = input_tree.bifurcating() # Required by most ancSR programs
if convert_to_bifurcating:
input_tree = ensure_root_is_bifurcating(input_tree)
# The below nutty-looking re-filtering step is necessary
# When ensuring the root is bifurcating, internal nodes can get moved to the tips
# So without additional filtering we get unannotated tip nodes
if filter_tree_by_table_entries:
input_tree = filter_tree_tips_by_presence_in_table(input_tree,trait_table_lines,delimiter=delimiter)
if enforce_min_branch_length:
input_tree = set_min_branch_length(input_tree,min_length = min_branch_length)
if opts.add_branch_length_to_root:
input_tree = add_branch_length_to_root(input_tree,root_name=input_tree.Name,root_length=min_branch_length)
input_tree.prune()
#if opts.verbose:
# print "Tree nodes after reformatting:"
# print_node_summary_table(input_tree)
# print "Convert to nexus is True?",convert_to_nexus is True
if convert_to_nexus is True:
lines = nexus_lines_from_tree(input_tree)
output_tree_file.write("\n".join(map(str,lines)))
else:
output_tree_file.write(input_tree.getNewick(with_distances=True))
output_tree_file.close()