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#!/usr/bin/env python
# File created on 12 Jan 2011
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 make_option
from os import makedirs
from qiime.util import (load_qiime_config,
parse_command_line_parameters,
get_options_lookup)
from qiime.parse import parse_qiime_parameters
from qiime.workflow import (run_pick_reference_otus_through_otu_table,
print_commands,
call_commands_serially,
print_to_stdout,
no_status_updates,
validate_and_set_jobs_to_start)
qiime_config = load_qiime_config()
options_lookup = get_options_lookup()
script_info = {}
script_info['brief_description'] = "Reference OTU picking/Shotgun UniFrac workflow."
script_info['script_description'] = "This script picks OTUs using a reference-based method and constructs an OTU table. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. If full-length genomes are provided as the reference sequences, this script applies the Shotgun UniFrac method."
script_info['script_usage'] = [
("","Pick OTUs, assign taxonomy, and create an OTU table against a reference set of OTUs.","%prog -i inseqs.fasta -r refseqs.fasta -o out -p qiime_parameters.txt -t taxa.txt"),
("","Pick OTUs and create an OTU table against a reference set of OTUs without adding taxonomy assignments.","%prog -i inseqs.fasta -r refseqs.fasta -o out -p qiime_parameters.txt")]
script_info['output_description']= ""
script_info['required_options'] = [
make_option('-i','--input_fp', help='the input sequences'),
make_option('-r','--reference_fp',help='the reference sequences'),
make_option('-o','--output_dir', help='the output directory'),
]
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('-t','--taxonomy_fp',help='the taxonomy map [default: %default]'),
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]'),
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
input_fp = opts.input_fp
reference_fp = opts.reference_fp
taxonomy_fp = opts.taxonomy_fp
output_dir = opts.output_dir
verbose = opts.verbose
print_only = opts.print_only
parallel = opts.parallel
# No longer checking that jobs_to_start > 2, but
# commenting as we may change our minds about this.
#if parallel: raise_error_on_parallel_unavailable()
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:
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_pick_reference_otus_through_otu_table(
input_fp,
reference_fp,
output_dir,
taxonomy_fp,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
status_update_callback=status_update_callback)
if __name__ == "__main__":
main()
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