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#!/usr/bin/env python
# File created on 16 Feb 2011
from __future__ import division
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
from qiime.util import make_option
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.submit_to_mgrast import parse_and_submit_params
from os import mkdir
from os.path import exists
options_lookup = get_options_lookup()
script_info = {}
script_info['brief_description'] = "This script submits a FASTA file to MG-RAST"
script_info['script_description'] = "This script takes a split-library FASTA file and generates individual FASTA files for each sample, then submits each sample FASTA file to MG-RAST, given the user provides an MG-RAST web-services authorization key and Project ID. To get a web-services authorization key, the user should have an account on MG-RAST. Once logged in, the user can go to their Account Management page and under Preferences they should click \'here\', where they will see a Web Services section where they can click on the \'generate new key\' if they have not already been provided one."
script_info['script_usage'] = [("Example","The user can submit a post-split-library FASTA file, which will be loaded and processed into MG-RAST under the users account ('-w') and project ('-p'), as follows:","submit_to_mgrast.py -i split_lib_seqs.fna -w user_mgrast_auth_key -p qiime_test_dataset -o ./output_dir")]
script_info['output_description']= "The resulting directory will contain all of the sample-separated FASTA files, along with a log html file, which informs the user of the jobs started on MG-RAST"
script_info['required_options'] = [\
options_lookup['fasta_as_primary_input'],
make_option('-w','--web_key_auth',help='the web services authorization key from MG-RAST'),
make_option('-p','--project_id',help='the title to be used for the project'),
options_lookup['output_dir'],
]
script_info['optional_options'] = [\
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
#define the variables
project_id=opts.project_id
files=opts.input_fasta_fp
key = opts.web_key_auth
#create directory path
if opts.output_dir:
if exists(opts.output_dir):
output_dir=opts.output_dir
else:
try:
mkdir(opts.output_dir)
output_dir=opts.output_dir
except OSError:
pass
else:
dir_path='./'
#call the main function
log_info=parse_and_submit_params(key,project_id,files,output_dir)
if __name__ == "__main__":
main()
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