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Viewing changes to qiime/parallel/assign_taxonomy.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/assign_taxonomy.py
 
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#!/usr/bin/env python
 
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from __future__ import division
 
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__author__ = "Jai Ram Rideout"
 
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__copyright__ = "Copyright 2012, The QIIME project"
 
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__credits__ = ["Jai Ram Rideout"]
 
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__license__ = "GPL"
 
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__version__ = "1.7.0"
 
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__maintainer__ = "Jai Ram Rideout"
 
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__email__ = "jai.rideout@gmail.com"
 
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__status__ = "Release"
 
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from cogent.app.formatdb import build_blast_db_from_fasta_path
 
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from qiime.parallel.util import ParallelWrapper
 
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class ParallelTaxonomyAssigner(ParallelWrapper):
 
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    _script_name = 'assign_taxonomy.py'
 
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    _input_splitter = ParallelWrapper._split_fasta
 
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    def _build_job_commands(self, tax_specific_param_str, fasta_fps,
 
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                            output_dir, params, job_prefix, working_dir,
 
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                            command_prefix='/bin/bash; ',
 
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                            command_suffix='; exit'):
 
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        """Generate assign_taxonomy.py commands which should be run."""
 
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        # Create basenames for each of the output files. These will be filled
 
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        # in to create the full list of files created by all of the runs.
 
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        out_filenames = [job_prefix + '.%d_tax_assignments.log', 
 
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                         job_prefix + '.%d_tax_assignments.txt']
 
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        # Create lists to store the results.
 
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        commands = []
 
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        result_filepaths = []
 
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        # Iterate over the input files.
 
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        for i, fasta_fp in enumerate(fasta_fps):
 
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            # Each run ends with moving the output file from the tmp dir to
 
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            # the output_dir. Build the command to perform the move here.
 
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            rename_command, current_result_filepaths = \
 
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                    self._get_rename_command([fn % i for fn in out_filenames],
 
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                                             working_dir, output_dir)
 
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            result_filepaths += current_result_filepaths
 
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            command = '%s %s %s -o %s -i %s %s %s' %\
 
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             (command_prefix,
 
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              self._script_name,
 
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              tax_specific_param_str,
 
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              working_dir,
 
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              fasta_fp,
 
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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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    def _write_merge_map_file(self,
 
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                              input_file_basename,
 
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                              job_result_filepaths,
 
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                              params,
 
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                              output_dir,
 
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                              merge_map_filepath,
 
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                              failures=False):
 
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        """ 
 
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        """
 
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        f = open(merge_map_filepath,'w')
 
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        out_filepaths = [
 
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         '%s/%s_tax_assignments.txt' % (output_dir,input_file_basename),
 
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         '%s/%s_tax_assignments.log' % (output_dir,input_file_basename)]
 
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        assignment_fps = []
 
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        log_fps = []
 
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        for fp in job_result_filepaths:
 
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            if fp.endswith('_tax_assignments.txt'):
 
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                assignment_fps.append(fp)
 
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            else:
 
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                log_fps.append(fp)
 
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        for in_files, out_file in\
 
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         zip([assignment_fps,log_fps],out_filepaths):
 
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            f.write('\t'.join(in_files + [out_file]))
 
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            f.write('\n')
 
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        f.close()
 
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class ParallelRdpTaxonomyAssigner(ParallelTaxonomyAssigner):
 
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    _job_prefix = 'RDP'
 
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    def _get_job_commands(self, fasta_fps, output_dir, params, job_prefix,
 
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                          working_dir, command_prefix=None,
 
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                          command_suffix='; exit'):
 
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        command_prefix = command_prefix or \
 
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            '/bin/bash; export RDP_JAR_PATH=%s; ' % params['rdp_classifier_fp']
 
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        rdp_params = '-m rdp -c %1.2f --rdp_max_memory %d ' % (
 
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                params['confidence'], params['rdp_max_memory'])
 
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        if params['id_to_taxonomy_fp'] and params['reference_seqs_fp']:
 
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            rdp_params += '-t %s -r %s' % (params['id_to_taxonomy_fp'],
 
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                                           params['reference_seqs_fp'])
 
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        return self._build_job_commands(rdp_params, fasta_fps, output_dir,
 
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                params, job_prefix, working_dir, command_prefix,
 
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                command_suffix)
 
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class ParallelBlastTaxonomyAssigner(ParallelTaxonomyAssigner):
 
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    _job_prefix = 'BTA'
 
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    def _precommand_initiation(self, input_fp, output_dir, working_dir, params):
 
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        if not params['blast_db']:
 
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            # Build the blast database from the reference_seqs_fp -- all procs
 
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            # will then access one db rather than create one per proc.
 
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            blast_db, db_files_to_remove = \
 
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                 build_blast_db_from_fasta_path(params['reference_seqs_fp'])
 
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            self.files_to_remove += db_files_to_remove
 
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            params['blast_db'] = blast_db
 
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    def _get_job_commands(self, fasta_fps, output_dir, params, job_prefix,
 
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                          working_dir, command_prefix=None,
 
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                          command_suffix='; exit'):
 
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        command_prefix = command_prefix or \
 
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            '/bin/bash; cd %s; export BLASTMAT=%s;' % (working_dir,
 
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            params['blastmat_dir'])
 
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        blast_params = '-m blast -e %s -b %s -t %s ' % (
 
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                params['e_value'], params['blast_db'],
 
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                params['id_to_taxonomy_fp'])
 
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        return self._build_job_commands(blast_params, fasta_fps, output_dir,
 
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                params, job_prefix, working_dir, command_prefix,
 
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                command_suffix)