def read_treemix_file2(filename_treeout,
filename_vertices,
filename_edges,
outgroup=None):
if filename_treeout.endswith('.gz'):
filename_treeout = unzip(filename_treeout)
if filename_vertices.endswith('.gz'):
filename_vertices = unzip(filename_vertices)
if filename_edges.endswith('.gz'):
filename_edges = unzip(filename_edges)
with open(filename_treeout, 'r') as f:
newick_tree = f.readline().rstrip()
admixtures = parse_admixtures2(map(str.rstrip, f.readlines()))
vertice_dictionary = read_vertices(filename_vertices)
print vertice_dictionary
edges = get_edge_lengths2(filename_edges)
#print newick_tree
tree = make_Rtree(edges, vertice_dictionary, admixtures)
print pretty_string(tree)
#tree=remove_children(tree)
if outgroup is not None:
tree = rearrange_root(tree, outgroup)
print 'after rearrangement'
print pretty_string(tree)
return tree
def make_single_files(filename,
blocksize,
no_blocks,
prefix='',
verbose_level='normal'):
assert (blocksize is not None) or (
no_blocks
is not None), 'Has to specify either block size or number of blocks'
filenames = []
if filename.endswith('.gz'):
filename = unzip(filename)
filename_reduced = prefix + filename.split(os.sep)[-1] + 'boot.'
with open(filename, 'r') as f:
first_line = f.readline()
lines = f.readlines()
#print lines
n = len(lines)
if no_blocks is not None:
blocksize = n / no_blocks
line_sets = get_partitions(lines, blocksize)
if verbose_level != 'silent':
print 'total SNPs=', n
print 'total blocksize', blocksize
#print 'no_blocks', no_blocks
print 'len(line_sets)', len(line_sets)
for i, lins in enumerate(line_sets):
new_filename = filename_reduced + str(i)
with open(new_filename, 'w') as g:
g.write(first_line)
g.writelines(lins)
gzipped_filename = gzip(new_filename, overwrite=True)
filenames.append(gzipped_filename)
return filenames, first_line.split()
def read_treemix_file(filename_treeout,
filename_vertices,
filename_edges,
outgroup=None):
np = new_node_naming_policy()
if filename_treeout.endswith('.gz'):
filename_treeout = unzip(filename_treeout)
if filename_vertices.endswith('.gz'):
filename_vertices = unzip(filename_vertices)
if filename_edges.endswith('.gz'):
filename_edges = unzip(filename_edges)
with open(filename_treeout, 'r') as f:
newick_tree = f.readline().rstrip()
admixtures = parse_admixtures(map(str.rstrip, f.readlines()))
edges = get_edge_lengths2(filename_edges)
#print newick_tree
tree, translates = parse_newick_tree(newick_tree)
vd = vertice_dictionary()
for adm_key, treemix_N_key in translates.items():
vd.insert_mapping(adm_key, treemix_N_key, 'AdmB', 'Treemix_N')
#print '-------------------------'
#print vd
vd, adm_vertices = match_vertices(filename_vertices, vd)
#matched_admixtures=match_admixtures(admixtures, adm_vertices)
# print '-------------------------'
# print vd
# print adm_vertices
edges = get_edge_lengths(filename_edges)
# print edges
tree = insert_children_in_tree(tree)
reverse_translates = {v: k for k, v in translates.items()}
# for k,c in translates.items():
# print k, ':', c
# for k,v in tree.items():
# print k,':',v
# print translates
# print admixtures
tree = add_admixtures(tree, vd, adm_vertices, edges, admixtures)
if outgroup is not None:
tree = rearrange_root(tree, outgroup)
return tree
def make_bootstrap_files(filename,
blocksize=None,
no_blocks=None,
bootstrap_samples=None,
prefix=''):
assert (blocksize is not None) or (
no_blocks
is not None), 'Has to specify either block size or number of blocks'
filenames = []
if filename.endswith('.gz'):
filename = unzip(filename)
filename_reduced = os.path.join(prefix,
filename.split(os.sep)[-1] + 'boot.')
with open(filename, 'r') as f:
first_line = f.readline()
lines = f.readlines()
n = len(lines)
if no_blocks is not None:
blocksize = n / no_blocks
line_sets = get_partitions(lines, blocksize)
print 'total SNPs=', n
print 'total blocksize', blocksize
print 'no_blocks', no_blocks
print 'bootstrap_samples', bootstrap_samples
print 'len(line_sets)', len(line_sets)
if bootstrap_samples is None:
bootstrap_samples = len(line_sets)
for i in range(bootstrap_samples):
new_filename = filename_reduced + str(i)
with open(new_filename, 'w') as g:
g.write(first_line)
bootstrap_inds = bootstrap_indices(len(line_sets))
for i in bootstrap_inds:
g.writelines(line_sets[i])
gzipped_filename = gzip(new_filename, overwrite=True)
filenames.append(gzipped_filename)
return filenames, first_line.split()
if options.input_type == 'tree':
tree = identifier_file_to_tree_clean(options.input_file)
if options.input_add:
with open(options.input_add, 'r') as f:
add = float(f.readline())
tree = add_outgroup(tree,
inner_node_name='new_node',
to_new_root_length=float(add),
to_outgroup_length=0,
outgroup_name=options.outgroup_name)
nodes = get_leaf_keys(tree)
assert all((a in nodes for a in options.populations
)), 'Requested population was not found in the tree'
subtree = get_subtree(tree, options.populations)
if not options.output_file:
options.output_file = options.input_file + '_'.join(
options.populations)
with open(options.output_file, 'w') as f:
f.write(' '.join(sorted(options.populations)) + '\n')
f.write(unique_identifier_and_branch_lengths(subtree))
if options.input_type == 'snps':
if options.input_file.endswith('.gz'):
options.input_file = unzip(options.input_file, overwrite=False)
df = pd.read_csv(options.input_file, usecols=options.populations, sep=' ')
if not options.output_file:
options.output_file = options.input_file + '_'.join(
options.populations)
df.to_csv(options.output_file, sep=' ', index=False)
gzip(options.output_file, overwrite=True)
def read_one_line(filename):
if filename.endswith('.gz'):
filename = unzip(filename)
with open(filename, 'r') as f:
return f.readline().rstrip().split()