make_tep.py

#!/usr/bin/env python
# File created on 15 Jun 2011
from __future__ import division

__author__ = "Meg Pirrung"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Meg Pirrung", "Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Meg Pirrung"
__email__ = "meganap@gmail.com"

from os.path import split,splitext
from qiime.util import parse_command_line_parameters, make_option
from qiime.util import load_qiime_config, create_dir, get_options_lookup
from qiime.format import format_tep_file_lines, format_jnlp_file_lines, \
                           format_te_prefs
from biom.parse import parse_biom_table
import os

options_lookup = get_options_lookup()

script_info = {}
script_info['brief_description'] = "Makes TopiaryExplorer project file"
script_info['script_description'] = "This script makes a TopiaryExplorer project file (.tep) and a jnlp file with the data location preloaded.\n\nWARNING: The jnlp file relies on an absolute path, if you move the .tep file, the generated jnlp will no longer work. However, you can still open the .tep file from your normal TopiaryExplorer install."

script_info['script_usage'] = []

script_info['script_usage'].append(("Example","Create .tep file and .jnlp file:","%prog -i otu_table.biom -m Fasting_Map.txt -t rep_set.tre"))

script_info['output_description']= "The result of this script is written to a .tep file and a .jnlp file, both with the name supplied by -o"

script_info['required_options'] = [
 options_lookup['otu_table_as_primary_input'],
 options_lookup['mapping_fp'],
 make_option('-t','--tree_fp', type="existing_filepath", help='path to tree')
]

script_info['optional_options'] = [
 options_lookup['output_dir'],
 make_option('-p','--prefs_file_fp', type="existing_filepath",
             help='path to prefs file'),\
 make_option('-w','--web_flag', action='store_true', default=False, 
             help='web codebase jnlp flag [default: %default]'),
 make_option('-u','--url',type="string",
             help='url path for the tep file. Note: when passing this flag, it will overwrite the supplied OTU table, Mapping and Tree files.')
]
script_info['version'] = __version__


def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)
    
    # get command line arguments
    otu_table_fp = opts.otu_table_fp
    mapping_fp = opts.mapping_fp
    tree_fp = opts.tree_fp
    output_dir = opts.output_dir
    output_basename = splitext(split(otu_table_fp)[1])[0]
    web_flag = opts.web_flag
    url = opts.url
    
    # create a generic output folder if not present
    if not output_dir:
        output_dir = 'make_tep_output/'
    create_dir(output_dir)    
    
    # open files for parsing
    otu_table_data = parse_biom_table(open(otu_table_fp, 'U'))
    mapping_lines = open(mapping_fp, 'U')    
    tree_lines = open(tree_fp, 'U')
    prefs_dict={}
    if opts.prefs_file_fp:
        prefs_fp = opts.prefs_file_fp
        # I don't like this eval statement
        prefs_dict = eval(open(prefs_fp,'U').read())
    
    # get the tep file lines
    lines = format_tep_file_lines(otu_table_data, mapping_lines, tree_lines, 
                               prefs_dict)
    
    # write tep file lines if url path not given
    tep_fp = '%s/%s.tep' % (output_dir,output_basename)
    if not url:
        # write tep file
        tepfile = open(tep_fp, 'w')
        tepfile.writelines(lines)
        tepfile.close()
    
    # get the jnlp file lines
    lines = format_jnlp_file_lines(web_flag, url, tep_fp)
    
    # write jnlp file
    jnlp_fp = '%s/%s.jnlp' % (output_dir,output_basename)
    jnlpfile = open(jnlp_fp, 'w')
    jnlpfile.writelines(lines)
    jnlpfile.close()
    
if __name__ == "__main__":
    main()