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Viewing changes to qiime/parallel/alpha_diversity.py

  • 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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qiime/parallel/alpha_diversity.py
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#!/usr/bin/env python
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# Author: Greg Caporaso (gregcaporaso@gmail.com)
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# alpha_diversity.py
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# File created on 13 Jul 2012
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from __future__ import division
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from os.path import split, splitext
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from qiime.parallel.util import get_rename_command
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__author__ = "Greg Caporaso"
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__copyright__ = "Copyright 2011, The QIIME Project"
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__credits__ = ["Greg Caporaso","Justin Kuczynski"] 
 
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__copyright__ = "Copyright 2011, The QIIME project"
 
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__credits__ = ["Greg Caporaso"]
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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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def get_job_commands(python_exe_fp,alpha_diversity_fp,tree_fp,job_prefix,\
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    metrics,input_fps,output_dir,working_dir,\
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    command_prefix=None,command_suffix=None):
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    """Generate alpha diversity commands to be submitted to cluster
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    """
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    command_prefix = command_prefix or '/bin/bash; '
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    command_suffix = command_suffix or '; exit'
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    commands = []
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    result_filepaths = []
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    for input_fp in input_fps:
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        input_path, input_fn = split(input_fp)
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        output_fn = 'alpha_%s' % input_fn
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        rename_command, current_result_filepaths = get_rename_command(\
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         [output_fn],working_dir,output_dir)
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        result_filepaths += current_result_filepaths
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        command = '%s %s %s -i %s -o %s -t %s -m %s %s %s' %\
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         (command_prefix,\
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          python_exe_fp,\
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          alpha_diversity_fp,\
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          input_fp,
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          working_dir + '/' + output_fn,
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          tree_fp,
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          metrics,
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          rename_command,
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          command_suffix)
 
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from os.path import join, split
 
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from qiime.parallel.util import ParallelWrapper
 
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class ParallelAlphaDiversity(ParallelWrapper):
 
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    _script_name = "alpha_diversity.py"
 
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    _job_prefix = 'ALDIV'
 
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    _input_splitter = ParallelWrapper._input_existing_filepaths
 
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    def _identify_files_to_remove(self,job_result_filepaths,params):
 
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        """ The output of the individual jobs are the files we want to keep
 
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        """
 
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        return []
 
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    def _get_job_commands(self,
 
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                          input_fps,
 
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                          output_dir,
 
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                          params,
 
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                          job_prefix,
 
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                          working_dir,
 
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                          command_prefix='/bin/bash; ',
 
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                          command_suffix='; exit'):
 
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        """Generate alpha diversity commands to be submitted to cluster
 
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        """
 
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        commands = []
 
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        result_filepaths = []
 
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        if params['tree_path']:
 
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            tree_str = '-t %s' % params['tree_path']
 
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        else:
 
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            tree_str = ''
 
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        for input_fp in input_fps:
 
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            input_path, input_fn = split(input_fp)
 
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            output_fn = 'alpha_%s' % input_fn
 
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            output_fn = output_fn.replace('.biom','.txt')
 
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            temp_fp = join(working_dir,output_fn)
 
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            rename_command, current_result_filepaths =\
 
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              self._get_rename_command([output_fn],working_dir,output_dir)
 
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            result_filepaths += current_result_filepaths
 
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            command = '%s %s -i %s -o %s %s -m %s %s %s' %\
 
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             (command_prefix,\
 
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              self._script_name,
 
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              input_fp,
 
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              temp_fp,
 
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              tree_str,
 
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              params['metrics'],
 
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              rename_command,
 
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              command_suffix)
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        commands.append(command)
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    return commands, result_filepaths
 
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            commands.append(command)
 
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        commands = self._merge_to_n_commands(commands,
 
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                                             params['jobs_to_start'],
 
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                                             command_prefix=command_prefix,
 
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                                             command_suffix=command_suffix)
 
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        return commands, result_filepaths
 
 
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