Generate sample ids for the office surface succession project.

generate_sample_ids.py

#!/usr/bin/env python
# File created on 29 May 2013
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.6.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "[email protected]"
__status__ = "Development"


from qiime.util import parse_command_line_parameters, make_option

script_info = {}
script_info['brief_description'] = ""
script_info['script_description'] = ""
script_info['script_usage'] = [("","","")]
script_info['output_description']= ""
script_info['required_options'] = [
 make_option('--cities',help="the city labels"),
 make_option('--max_timepoint',type='int',help="the maximum timepoint to create labels until")
]
script_info['optional_options'] = []
script_info['version'] = __version__



def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)

    cities = opts.cities
    buildings = map(str,[1,2,3])
    plate_locations = ['C','F','W']
    rows = map(str,[3])
    sample_types = ['Ca','Ce','Dr']
    max_timepoint = opts.max_timepoint
    
    for city in cities:
        for timepoint in range(1,max_timepoint+1):
            for building in buildings:
                for plate_location in plate_locations:
                    for row in rows:
                        for sample_type in sample_types:
                            print '.'.join([city+building+plate_location,row,sample_type,"%03d" % timepoint])
    


if __name__ == "__main__":
    main()