Public Member Functions
public	options ()

public	query_identity_threshold ()

public	target_identity_threshold ()

public	submit_exonerate ()

public	global_jobid ()

public	submit_depend_job ()

public	submit_qsub ()

Detailed Description

Definition at line 5 of file PBSExonerateGappedBest1.pm.

Member Function Documentation

◆ global_jobid()

public XrefMapper::Methods::PBSExonerateGappedBest1::global_jobid ( )

Undocumented method

Code:

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◆ options()

public XrefMapper::Methods::PBSExonerateGappedBest1::options ( )

Undocumented method

Code:

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◆ query_identity_threshold()

public XrefMapper::Methods::PBSExonerateGappedBest1::query_identity_threshold ( )

Undocumented method

Code:

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◆ submit_depend_job()

public XrefMapper::Methods::PBSExonerateGappedBest1::submit_depend_job ( )

Undocumented method

Code:

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◆ submit_exonerate()

public XrefMapper::Methods::PBSExonerateGappedBest1::submit_exonerate ( )

Undocumented method

Code:

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sub submit_exonerate{
  my ($self, $query, $target, $root_dir, @options) = @_;
 
  # Exonerate can run individual chunks of a large job.
  # Determine the number of chunks that will be used, and add to total
  my $num_jobs 
      = XrefMapper::Methods::ExonerateBasic::calculate_num_jobs($query);
  $self->jobcount($self->jobcount()+$num_jobs);
 
  $num_jobs || return; # Check we have jobs to run
 
  # Build a template representing the exonerate command
  my $options_str = join( ' ', @options );
  my $shell_command = <<"EOF";
#!/bin/sh
$exonerate_path \\
--target $target \\
--query $query \\
--querychunktotal $num_jobs \\
--querychunkid %d \\
--showvulgar FALSE \\
--showalignment FALSE \\
--ryo "xref:%%qi:%%ti:%%ei:%%ql:%%tl:%%qab:%%qae:%%tab:%%tae:%%C:%%s\\n" \\
$options_str \\
| grep '^xref'
exit
EOF
 
  #warn( sprintf $shell_command, 1 );
 
  # Determine the output filename
  my $host = Sys::Hostname::hostname;
  my $query_alphabet = $query =~ /peptide.fasta$/ ? 'peptide' : 'dna';
  my $outfile_root = sprintf( "%s:%s/%s_%s",
                              $host,
                              $root_dir,
                              $self->get_class_name(), 
                              $query_alphabet );
  
  # Run PBS qsub for each job chunk.
  # First set a job that depends on the completion of all other jobs
  my $jobid = $self->submit_qsub( q( echo 'sleep 1' ), 
                                  [ -W => "depend=on:$num_jobs" ] );
 
  # Run each job chunk
  my $jobname = join '.', 'X', ( $host =~ /^(\w+)/ ), $$; 
  foreach( my $i=1; $i<=$num_jobs; $i++ ){
 
    my $outfile = sprintf( '%s_%s.map', $outfile_root, $i );
    my $errfile = sprintf( '%s_%s.err', $outfile_root, $i );
 
    my $chunkid = $self->submit_qsub
        ( sprintf( $shell_command, $i ),
          [ '-N' => $jobname, 
            '-W' => "depend=beforeany:$jobid", 
            '-o' => $outfile, 
            '-e' => $errfile ] );
  }
 
  # BasicMapper calls a method called 'submit_depend_job' that waits
  # till all the lsf jobs have completed. We're not using LSF, so this
  # approach does not work. Solution: wait here until all jobs are done.
  # Not as efficient for a large cluster, but we may have enough work to
  # do to saturate a small one. TODO: abstract 'submit_depend_job' to the 
  # Method class instances.
 
  $self->global_jobid( $jobid );
  #$self->submit_depend_job( $jobid );
 
  return $jobid;
}

◆ submit_qsub()

public XrefMapper::Methods::PBSExonerateGappedBest1::submit_qsub ( )

Undocumented method

Code:

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◆ target_identity_threshold()

public XrefMapper::Methods::PBSExonerateGappedBest1::target_identity_threshold ( )

Undocumented method

Code:

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The documentation for this class was generated from the following file:

ensembl/misc-scripts/xref_mapping/XrefMapper/Methods/PBSExonerateGappedBest1.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ global_jobid()

◆ options()

◆ query_identity_threshold()

◆ submit_depend_job()

◆ submit_exonerate()

◆ submit_qsub()

◆ target_identity_threshold()