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#!/usr/bin/env python
# File created on 04 Jan 2010.
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from os import makedirs
from qiime.util import load_qiime_config
from qiime.parse import parse_qiime_parameters
from qiime.workflow import (run_qiime_alpha_rarefaction, print_commands,
call_commands_serially, print_to_stdout, no_status_updates,
validate_and_set_jobs_to_start)
qiime_config = load_qiime_config()
#alpha_rarefaction.py
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""A workflow script for performing alpha rarefaction"""
script_info['script_description']="""
The steps performed by this script are:
1. Generate rarefied OTU tables;
2. Compute alpha diversity metrics for each rarefied OTU table;
3. Collate alpha diversity results;
4. Generate alpha rarefaction plots.
"""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example""","""""","""alpha_rarefaction.py -o rare1 -i otu_table.txt -t inseqs1_rep_set.tre -m inseqs1_mapping.txt -p custom_parameters.txt"""))
script_info['output_description']="""The results of this script is a folder ("rare1/") containing rarefied otu tables, alpha-diversity for each otu table, a file containing the results from collating the alpha-diversity results and a folder containing the rarefaction plots."""
script_info['required_options']=[\
make_option('-i','--otu_table_fp',\
help='the input otu table [REQUIRED]'),\
make_option('-m','--mapping_fp',\
help='path to the mapping file [REQUIRED]'),\
make_option('-o','--output_dir',\
help='the output directory [REQUIRED]'),
]
script_info['optional_options']=[\
make_option('-p','--parameter_fp',
help='path to the parameter file, which specifies changes'+\
' to the default behavior. '+\
'See http://www.qiime.org/documentation/file_formats.html#qiime-parameters .'+\
' [if omitted, default values will be used]'),
make_option('-n','--num_steps',type='int',\
help='number of steps (or rarefied OTU table sizes) to make between '+\
'min and max counts [default: %default]',default=10),\
make_option('-f','--force',action='store_true',\
dest='force',help='Force overwrite of existing output directory'+\
' (note: existing files in output_dir will not be removed)'+\
' [default: %default]'),\
make_option('-w','--print_only',action='store_true',\
dest='print_only',help='Print the commands but don\'t call them -- '+\
'useful for debugging [default: %default]',default=False),\
make_option('-a','--parallel',action='store_true',\
dest='parallel',default=False,\
help='Run in parallel where available [default: %default]'),\
make_option('-t','--tree_fp',\
help='path to the tree file [default: %default; '+\
'REQUIRED for phylogenetic measures]'),
make_option('--min_rare_depth',type='int',\
help='the lower limit of rarefaction depths '+\
'[default: %default]',default=10),
make_option('-e','--max_rare_depth',type='int',\
help='the upper limit of rarefaction depths '+\
'[default: median sequence/sample count]'),
options_lookup['jobs_to_start_workflow']]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
otu_table_fp = opts.otu_table_fp
output_dir = opts.output_dir
mapping_fp = opts.mapping_fp
tree_fp = opts.tree_fp
num_steps = opts.num_steps
verbose = opts.verbose
print_only = opts.print_only
parallel = opts.parallel
min_rare_depth = opts.min_rare_depth
max_rare_depth = opts.max_rare_depth
if opts.parameter_fp:
try:
parameter_f = open(opts.parameter_fp)
except IOError:
raise IOError,\
"Can't open parameters file (%s). Does it exist? Do you have read access?"\
% opts.parameter_fp
params = parse_qiime_parameters(parameter_f)
else:
params = parse_qiime_parameters([])
# empty list returns empty defaultdict for now
jobs_to_start = opts.jobs_to_start
default_jobs_to_start = qiime_config['jobs_to_start']
validate_and_set_jobs_to_start(params,
jobs_to_start,
default_jobs_to_start,
parallel,
option_parser)
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
print "Output directory already exists. Please choose "+\
"a different directory, or force overwrite with -f."
exit(1)
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_qiime_alpha_rarefaction(otu_table_fp=otu_table_fp,\
mapping_fp=mapping_fp,\
output_dir=output_dir,\
command_handler=command_handler,\
params=params,
qiime_config=qiime_config,\
tree_fp=tree_fp,\
num_steps=num_steps,\
parallel=parallel,\
min_rare_depth=min_rare_depth,
max_rare_depth=max_rare_depth,
status_update_callback=status_update_callback)
if __name__ == "__main__":
main()
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