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#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Justin Kuczynski, Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from os.path import splitext
from qiime.util import make_option
from qiime.util import parse_command_line_parameters
from qiime.make_phylogeny import tree_module_names, tree_method_constructors,\
CogentTreeBuilder
import warnings
script_info={}
script_info['brief_description']="""Make Phylogeny"""
script_info['script_description']="""Many downstream analyses require that the phylogenetic tree relating the OTUs in a study be present. The script make_phylogeny.py produces this tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs, by default using FastTree (Price, Dehal, & Arkin, 2009)."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Examples:""","""A simple example of make_phylogeny.py is shown by the following command, where we use the default tree building method (fasttree) and write the file to the current working directory without a log file:""","""make_phylogeny.py -i repr_set_seqs_aligned_pfiltered.fasta -o rep_phylo.tre"""))
script_info['script_usage'].append(("""""","""Alternatively, if the user would prefer using another tree building method (i.e. clearcut (Sheneman, Evans, & Foster, 2006)), then they could use the following command:""","""make_phylogeny.py -i repr_set_seqs_aligned_pfiltered.fasta -t clearcut"""))
script_info['script_usage'].append(("""""","""Note: For whichever method used, the 3rd party program must be properly installed on the user's computer.""",""""""))
script_info['output_description']="""The result of make_phylogeny.py consists of a newick formatted tree file (.tre) and optionally a log file. The tree file is formatted using the Newick format and this file can be viewed using most tree visualization tools, such as TopiaryTool, FigTree, etc.
The tips of the tree are the first word from the input sequences from the fasta file, e.g.: '>101 PC.481_71 RC:1..220' is represented in the tree as '101'."""
script_info['required_options']=[
make_option('-i','--input_fp',action='store',
type='string',dest='input_fp',help='Path to read '+\
'input fasta alignment, only first word in defline will be considered')
]
valid_root_methods = ['midpoint','tree_method_default']
script_info['optional_options']=[\
make_option('-t','--tree_method',action='store',
help='Method for tree building. Valid choices are: '+\
', '.join(tree_module_names.keys())+\
' [default: %default]', default='fasttree'),
make_option('-o','--result_fp',action='store',
help='Path to store '+\
'result file [default: <input_sequences_filename>.tre]'),
make_option('-l','--log_fp',action='store',
help='Path to store '+\
'log file [default: No log file created.]'),
make_option('-r','--root_method',action='store',
help='method for choosing root of phylo tree'+\
' Valid choices are: '+ ', '.join(valid_root_methods) +\
' [default: tree_method_default]',
default='tree_method_default'),
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not (opts.tree_method in tree_method_constructors or
opts.tree_method in tree_module_names):
option_parser.error(\
'Invalid alignment method: %s.\nValid choices are: %s'\
% (opts.tree_method,\
' '.join(tree_method_constructors.keys() +
tree_module_names.keys())))
try:
tree_builder_constructor =\
tree_method_constructors[opts.tree_method]
tree_builder_type = 'Constructor'
params = {}
tree_builder = tree_builder_constructor(params)
except KeyError:
tree_builder = CogentTreeBuilder({
'Module':tree_module_names[opts.tree_method],
'Method':opts.tree_method
})
tree_builder_type = 'Cogent'
input_seqs_filepath = opts.input_fp
result_path = opts.result_fp
if not result_path: # empty or None
fpath, ext = splitext(input_seqs_filepath) # fpath omits extension
result_path = fpath + ".tre"
open(result_path,'w').close() # touch
log_path = opts.log_fp
if log_path != None:
open(log_path,'w').close()
if tree_builder_type=='Constructor':
tree_builder(input_seqs_filepath,\
result_path=result_path,log_path=log_path,failure_path=failure_path)
elif tree_builder_type=='Cogent':
tree_builder(result_path, aln_path=input_seqs_filepath,
log_path=log_path, root_method=opts.root_method)
if __name__ == "__main__":
main()
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