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Viewing changes to qiime/parallel/align_seqs.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/align_seqs.py
 
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#!/usr/bin/env python
 
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# File created on 07 Jul 2012
 
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from __future__ import division
 
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__author__ = "Greg Caporaso"
 
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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__ = "1.7.0"
 
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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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from cogent.app.formatdb import build_blast_db_from_fasta_path
 
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from qiime.align_seqs import compute_min_alignment_length
 
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from qiime.parallel.util import ParallelWrapper
 
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class ParallelAlignSeqsPyNast(ParallelWrapper):
 
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    _script_name = "align_seqs.py"
 
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    _job_prefix = 'ALIGN'
 
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    _input_splitter = ParallelWrapper._split_fasta
 
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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['template_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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        if params['min_length'] < 0:
 
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            params['min_length'] = compute_min_alignment_length(\
 
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                                    open(input_fp,'U'))
 
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    def _get_job_commands(self,
 
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                          fasta_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 PyNAST commands which should be submitted to cluster
 
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        """
 
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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_aligned.fasta', 
 
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                         job_prefix + '.%d_failures.fasta',
 
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                         job_prefix + '.%d_log.txt']
 
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        # Initialize the command_prefix and command_suffix
 
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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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        # Create lists to store the results
 
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        commands = []
 
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        result_filepaths = []
 
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        # If there is a value for blast_db, pass it. If not, it
 
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        # will be created on-the-fly. Note that on-the-fly blast dbs
 
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        # are created with a string of random chars in the name, so this is safe.
 
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        # They shouldn't overwrite one another, and will be cleaned up.
 
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        if params['blast_db']:
 
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            blast_str = '-d %s' % params['blast_db']
 
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        else:
 
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            blast_str = ''
 
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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 = self._get_rename_command(\
 
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             [fn % i for fn in out_filenames],working_dir,output_dir)
 
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            result_filepaths += current_result_filepaths
 
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            command = \
 
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             '%s %s %s -p %1.2f -e %d -m pynast -t %s -a %s -o %s -i %s %s %s' %\
 
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             (command_prefix,
 
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              self._script_name,
 
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              blast_str,
 
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              params['min_percent_id'],
 
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              params['min_length'],
 
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              params['template_fp'],\
 
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              params['pairwise_alignment_method'],
 
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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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        f = open(merge_map_filepath,'w')
 
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        out_filepaths = ['%s/%s_aligned.fasta' % (output_dir,input_file_basename),
 
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                         '%s/%s_failures.fasta' % (output_dir,input_file_basename),
 
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                         '%s/%s_log.txt' % (output_dir,input_file_basename)]
 
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        aligned_fps = []
 
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        failures_fps = []
 
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        log_fps = []
 
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        for fp in job_result_filepaths:
 
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            if fp.endswith('_aligned.fasta'):
 
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                aligned_fps.append(fp)
 
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            elif fp.endswith('_failures.fasta'):
 
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                failures_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([aligned_fps,failures_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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b'\\ No newline at end of file'