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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
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scripts/identify_missing_files.py
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__author__ = "Greg Caporaso"
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__copyright__ = "Copyright 2011, The QIIME project"
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__credits__ = ["Greg Caporaso"]
 
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__credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
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__license__ = "GPL"
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__version__ = "1.5.0"
 
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__version__ = "1.7.0"
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__maintainer__ = "Greg Caporaso"
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__email__ = "gregcaporaso@gmail.com"
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__status__ = "Release"
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from qiime.util import parse_command_line_parameters, make_option
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from os.path import exists
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script_info = {}
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script_info['brief_description'] = "This script checks for the existence expected file in parallel runs."
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script_info['script_description'] = "This script checks for the existence expected file in parallel runs, and is useful for checking the status of a parallel run or for finding out what poller.py is waiting on in a possibly failed run."
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script_info['script_usage'] = [("","Check for the existence of files listed in the expected_out_files.txt from a PyNAST alignment run, and print a warning for any that are missing.","identify_missing_files.py -e ALIGN_BQ7_/expected_out_files.txt")]
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script_info['output_description']= ""
 
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script_info['brief_description'] = "This script checks for the existence of expected files in parallel runs."
 
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script_info['script_description'] = "This script checks for the existence of expected files in parallel runs, and is useful for checking the status of a parallel run or for finding out what poller.py is waiting on in a possibly failed run."
 
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script_info['script_usage'] = [("Example",
 
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"Check for the existence of files listed in expected_out_files.txt from a "
 
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"PyNAST alignment run, and print a warning for any that are missing.",
 
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"%prog -e ALIGN_BQ7_/expected_out_files.txt")]
 
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script_info['output_description']= """
 
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This script does not create any output files.
 
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"""
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script_info['required_options'] = [
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 make_option('-e','--expected_out_fp',
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             type="existing_filepath",
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             help='the list of expected output files'),
 
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             help='the list of expected output files')
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]
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script_info['optional_options'] = []
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script_info['version'] = __version__
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def main():
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    option_parser, opts, args =\
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       parse_command_line_parameters(**script_info)
 
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    option_parser, opts, args = parse_command_line_parameters(**script_info)
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    filepaths = [l.strip() for l in open(opts.expected_out_fp,'U')]
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    all_exist = True
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    if all_exist:
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        print "All filepaths exist."
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if __name__ == "__main__":
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    main()
 
 
b'\\ No newline at end of file'
 
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    main()