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#!/usr/bin/env python
# File created on 27 Oct 2009.
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Kyle Bittinger"]
__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_qiime_data_preparation, 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'] = """A workflow script for picking OTUs through building OTU tables"""
script_info['script_description'] = """This script takes a sequence file and performs all processing steps through building the OTU table."""
script_info['script_usage'] = []
script_info['script_usage'].append(("""Simple example""","""The following command will start an analysis on inseq1.fasta (-i), which is a post-split_libraries fasta file. The sequence identifiers in this file should be of the form <sample_id>_<unique_seq_id>. The following steps, corresponding to the preliminary data preparation, are applied.
1. Pick OTUs with uclust at similarity of 0.97;
2. Pick a representative set with the most_abundant method;
3. Align the representative set with PyNAST;
4. Assign taxonomy with RDP classifier;
5. Filter the alignment prior to tree building - remove positions which are all gaps, and specified as 0 in the lanemask;
6. Build a phylogenetic tree with FastTree;
7. Build an OTU table.
All output files will be written to the directory specified by -o, and
subdirectories as appropriate.
""","""pick_otus_through_otu_table.py -i inseqs1.fasta -o wf1/ -p custom_parameters.txt"""))
script_info['output_description'] ="""This script will produce an OTU mapping file (pick_otus.py), a representative set of sequences (FASTA file from pick_rep_set.py), a sequence alignment file (FASTA file from align_seqs.py), taxonomy assignment file (from assign_taxonomy.py), a filtered sequence alignment (from filter_alignment.py), a phylogenetic tree (Newick file from make_phylogeny.py) and an OTU table (from make_otu_table.py)."""
script_info['required_options'] = [
make_option('-i','--input_fp',
help='the input fasta 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('-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
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:
# 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_data_preparation(
input_fp,
output_dir,
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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