#!/opt/anaconda1anaconda2anaconda3/bin/python
# File created on 04 Jan 2010.
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"

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.util import (print_commands,
                                 call_commands_serially,
                                 print_to_stdout,
                                 no_status_updates,
                                 validate_and_set_jobs_to_start)
from qiime.workflow.downstream import run_beta_diversity_through_plots


#beta_diversity_through_3d_plots.py
qiime_config = load_qiime_config()
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""A workflow script for computing beta diversity distance matrices and generating PCoA plots"""
script_info['script_description']="""This script will perform beta diversity, principal coordinate anlalysis, and generate a preferences file along with 3D PCoA Plots.
"""
script_info['script_usage']=[]

script_info['script_usage'].append(("""Example:""","""Given an OTU table, a phylogenetic tree, an even sampling depth, and a mapping file, perform the following steps: 1. Randomly subsample otu_table.biom to even number of sequences per sample (100 in this case); 2. Compute a weighted and unweighted unifrac distance matrcies (can add additional metrics by passing a parameters file via -p); 3. Peform a principal coordinates analysis on the result of Step 2; 4. Generate a 2D and 3D plots for all mapping fields.""","""%prog -i otu_table.biom -o bdiv_even100/ -t rep_set.tre -m Fasting_Map.txt -e 100"""))

script_info['script_usage_output_to_remove'] = ['bdiv_even100']

script_info['output_description']="""This script results in a distance matrix (from beta_diversity.py), a principal coordinates file (from principal_coordinates.py), a preferences file (from make_prefs_file.py) and folders containing the resulting PCoA plots (accessible through html files)."""

script_info['required_options']=[\
 make_option('-i','--otu_table_fp',type='existing_filepath',
            help='the input biom table [REQUIRED]'),
 make_option('-m','--mapping_fp',type='existing_filepath',
            help='path to the mapping file [REQUIRED]'),
 make_option('-o','--output_dir',type='new_dirpath',
            help='the output directory [REQUIRED]'),
]
script_info['optional_options']=[
 make_option('-t','--tree_fp',type='existing_filepath',
            help='path to the tree file [default: %default; '+\
            'REQUIRED for phylogenetic measures]'),
 make_option('-p','--parameter_fp',type='existing_filepath',
    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('--color_by_all_fields',
            help='plots will have coloring for all mapping fields '+\
            '[default: %default; only include fields with greater than one value '+\
            'and fewer values than the number of samples]',
            default=False,action='store_true'),
 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]'),
 make_option('-e','--seqs_per_sample',type='int',
     help='depth of coverage for even sampling [default: %default]'),
 make_option('--suppress_emperor_plots',action='store_true',
        help='Do not generate emperor plots [default: %default]',
        default=False),
 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
    
    otu_table_fp = opts.otu_table_fp
    output_dir = opts.output_dir
    mapping_fp = opts.mapping_fp
    tree_fp = opts.tree_fp
    verbose = opts.verbose
    print_only = opts.print_only
    seqs_per_sample = opts.seqs_per_sample
    
    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, 'U')
        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)
        parameter_f.close()
    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.
            option_parser.error("Output directory already exists. Please choose"
                " a different directory, or force overwrite with -f.")

    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_beta_diversity_through_plots(otu_table_fp=otu_table_fp,
     mapping_fp=mapping_fp,
     output_dir=output_dir,
     command_handler=command_handler,
     params=params,
     qiime_config=qiime_config,
     color_by_interesting_fields_only=not opts.color_by_all_fields,
     sampling_depth=seqs_per_sample,
     tree_fp=tree_fp,
     parallel=parallel,
     suppress_emperor_plots=opts.suppress_emperor_plots,
     status_update_callback=status_update_callback)

if __name__ == "__main__":
    main()
