Public Member Functions
public	new ()

public	mapper ()

public Scalar	jobcount ()

public void	run ()

public List	options ()

public	resubmit_exonerate ()

public The	submit_exonerate ()

public The	calculate_num_jobs ()

public	get_class_name ()

public	check_err ()

public	query_identity_threshold ()

public	target_identity_threshold ()

Detailed Description

Definition at line 5 of file ExonerateBasic.pm.

Member Function Documentation

◆ calculate_num_jobs()

public The XrefMapper::Methods::ExonerateBasic::calculate_num_jobs ( )

  Args       : Query file name
  Example    :

none

  Description: Calculate the number of LSF jobs to submit based on the size of the query file.
  Returntype : The number of jobs.
  Exceptions : none
  Caller     : general

Code:

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◆ check_err()

public XrefMapper::Methods::ExonerateBasic::check_err ( )

Undocumented method

Code:

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◆ get_class_name()

public XrefMapper::Methods::ExonerateBasic::get_class_name ( )

Undocumented method

Code:

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◆ jobcount()

public Scalar XrefMapper::Methods::ExonerateBasic::jobcount ( )

 
  Arg [1]    : (optional) 
  Example    :

$mapper->jobcount(1004);

  Description: Getter / Setter for number of jobs submitted. 
  Returntype : scalar
  Exceptions : none

Code:

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◆ mapper()

public XrefMapper::Methods::ExonerateBasic::mapper ( )

Undocumented method

Code:

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◆ new()

public XrefMapper::Methods::ExonerateBasic::new ( )

Undocumented method

Code:

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◆ options()

public List XrefMapper::Methods::ExonerateBasic::options ( )

  Args       : none
  Example    :

none

  Description: Options to pass to exonerate. Override as appropriate.
  Returntype : List of strings.
  Exceptions : none
  Caller     : general

Code:

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◆ query_identity_threshold()

public XrefMapper::Methods::ExonerateBasic::query_identity_threshold ( )

Undocumented method

Code:

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◆ resubmit_exonerate()

public XrefMapper::Methods::ExonerateBasic::resubmit_exonerate ( )

Code:

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sub resubmit_exonerate {
  my ($self, $mapper, $command, $outfile, $errfile, $job_id, $array_number, $root_dir) = @_;
 
 
 
  my ($junk,$query, $target, @rest) = split(/\s+/,$command);
 
  my $disk_space_needed = (stat($query))[7]+(stat($target))[7];
  
  $disk_space_needed /= 1024000; # convert to MB
  $disk_space_needed = int($disk_space_needed);
  $disk_space_needed += 1;
  
  my $unique_name = $self->get_class_name() . "_" . time();
  
  my $exe_file = $root_dir."/resub_".$job_id."_".$array_number;
  open(my $rh, ">", $exe_file) || die "Could not open file $exe_file";
  
  my $lsf_profile = '/usr/local/lsf/conf/profile.lsf';
  if (-e $lsf_profile) {
    print $rh ". $lsf_profile\n";
  }
  print $rh $command."\n";
 
  close $rh;
 
  chmod 0755, $exe_file;
 
  my $queue = $self->mapper->farm_queue || 'production-rh74';
  
  my $usage = '-M 1500 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" -J "'.$unique_name.'"';
  $queue and $usage .=  ' -q '. $queue;
 
  my $com = "bsub $usage -o $root_dir/$outfile -e $root_dir/$errfile ".$exe_file;
 
  if($mapper->nofarm){
    print "Running job locally for job number $job_id [$array_number]\n" if($mapper->verbose);
    my $line = `$exe_file`;
    my $sth = $mapper->xref->dbc->prepare('update mapping_jobs set status = "SUBMITTED"'." where job_id = $job_id and array_number = $array_number");
    $sth->execute();
    $sth->finish;
    return 1;
  }
 
 
  my $line = `$com`;
 
  my $jobid  = 0;
  if ($line =~ /^Job <(\d+)> is submitted/) {
     $jobid = $1;
     print "LSF job ID for main mapping job: $jobid (job array with 1 job ($array_number))\n" if($mapper->verbose);
  }
 
 
  if (!$jobid) {
    # Something went wrong
    warn("Job submission failed:\n$@\n");
    print STDERR "bsub command was $com\n";
    print STDERR $line."\n";
    return 0;
  }
  else{
    # write details of job to database
    my $sth = $mapper->xref->dbc->prepare('update mapping_jobs set status = "SUBMITTED"'." where job_id = $job_id and array_number = $array_number");
    $sth->execute();
    $sth->finish;
  }
  
  return $jobid;
 
}

◆ run()

public void XrefMapper::Methods::ExonerateBasic::run ( )

  Arg[1]     : Query filename to pass to exonerate; this should be the XREF file.
  Arg[2]     : Target filename to pass to exonerate; this should be the ENSEMBL file.
  Example    :

none

  Description: Run exonerate with default options.
  Returntype : none
  Exceptions : none
  Caller     : general

Code:

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◆ submit_exonerate()

public The XrefMapper::Methods::ExonerateBasic::submit_exonerate ( )

  Args       : none
  Example    :

none

  Description: Submit a *single* mapping job array to exonerate.
  Returntype : The name of the job array submitted to LSF. Can be used in depend job.
  Exceptions : none
  Caller     : general

Code:

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sub submit_exonerate {
 
  my ($self, $query, $target, $mapper, @options) = @_;
 
 
  my $root_dir = $mapper->core->dir;
 
  my $queryfile = basename($query);
  my $targetfile = basename($target);
 
  my $prefix = $root_dir . "/" . basename($query);
  $prefix =~ s/\.\w+$//;
 
  my ($ensembl_type) = $prefix =~ /.*_(dna|peptide)$/; # dna or prot
  my $options_str = join(" ", @options);
 
  my $unique_name = $self->get_class_name() . "_" . time();
 
  my $disk_space_needed = (stat($query))[7]+(stat($target))[7];
 
  $disk_space_needed /= 1024000; # convert to MB
  $disk_space_needed = int($disk_space_needed);
  $disk_space_needed += 1;
 
  my $num_jobs = calculate_num_jobs($query);
 
 
  my $exe = $self->mapper->exonerate || $exonerate_path;
 
 
  if(defined($mapper->nofarm)){
    my $output = $self->get_class_name() . "_" . $ensembl_type.  "_1.map";
    my $cmd = <<EON;
$exe $query $target --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" $options_str | grep '^xref' > $root_dir/$output
EON
    print "none farm command is $cmd\n" if($mapper->verbose);
 
 
    # write details of job to database
    
    my $sth = $mapper->xref->dbc->prepare("insert into process_status (status, date) values('mapping_submitted',now())");
    $sth->execute();
    $sth->finish;
    
    my $jobid = 1;
    if($ensembl_type eq "peptide"){
      $jobid = 2;
    }
 
    for( my $i=1; $i<=1; $i++){
      my $command = "$exe $query $target --showvulgar false --showalignment FALSE --ryo ".
    '"xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\\\n"'." $options_str | grep ".'"'."^xref".'"'." > $root_dir/$output";
      my $insert = "insert into mapping (job_id, type, command_line, percent_query_cutoff, percent_target_cutoff, method, array_size) values($jobid, '$ensembl_type', '$command',".
                       $self->query_identity_threshold.", ".$self->target_identity_threshold.", '".$self->get_class_name()."', $i)";
      
      $sth = $mapper->xref->dbc->prepare($insert);
      $sth->execute;
      $sth->finish;
      
      $sth = $mapper->xref->dbc->prepare("insert into mapping_jobs (root_dir, map_file, status, out_file, err_file, array_number, job_id) values (?,?,?,?,?,?,?)");
      
      my $map_file = $self->get_class_name()."_".$ensembl_type."_".$i.".map";
      my $out_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".out";
      my $err_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".err";
      $sth->execute($root_dir, $map_file, 'SUBMITTED', $out_file, $err_file, $i, $jobid);
    }
    $sth->finish;
    
 
    system($cmd);
    $self->jobcount(1);
    return "nofarm";
  }
 
 
  # array features barf if just one job 
  if($num_jobs == 1){
    $num_jobs++;
  }
 
  $self->jobcount($self->jobcount()+$num_jobs);
 
 
 
  my $output = $self->get_class_name() . "_" . $ensembl_type . "_" . "\$LSB_JOBINDEX.map";
 
  my $queue = $self->mapper->farm_queue || 'production-rh74';
 
 
  my $usage = '-M 1500 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" '.'-J "'.$unique_name.'[1-'.$num_jobs.']%200" -o '.$prefix.'.%J-%I.out -e  '.$prefix.'.%J-%I.err';
  $queue and $usage = "-q $queue " . $usage;
 
 
  my $command = $exe." ".$query." ".$target.' --querychunkid $LSB_JOBINDEX --querychunktotal '.$num_jobs.' --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" '.$options_str;
  $command .= " | grep '^xref' > $root_dir/$output";
 
  my $exe_file = $root_dir."/".$unique_name.".submit";
  open(my $rh,">", $exe_file) || die "Could not open file $exe_file";
  
  my $lsf_conf = "/usr/local/lsf/conf/profile.lsf";
  if (-e $lsf_conf) {
    print $rh ". $lsf_conf\n";
  }
  print $rh $command."\n";
 
  close $rh;
 
  chmod 0755, $exe_file;
 
  my $com = "bsub $usage $exe_file";
 
  my $line = `$com`;
 
  my $jobid  = 0;
  if ($line =~ /^Job <(\d+)> is submitted/) {
     $jobid = $1;
     print "LSF job ID for main mapping job: $jobid, name $unique_name with $num_jobs arrays elements)\n" if($mapper->verbose);
  }
 
 
  if (!$jobid) {
    # Something went wrong
    warn("Job submission failed:\n$@\n");
    print STDERR "bsub command was $com\n";
    print STDERR $line."\n";
    return 0;
  } 
  else{
    # write details of job to database
    my $command = "$exe $query $target --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo ".
      '"xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\\\n"'." $options_str | grep ".'"'."^xref".'"'." > $root_dir/$output";
 
    my $sth = $mapper->xref->dbc->prepare("insert into process_status (status, date) values('mapping_submitted',now())");
    $sth->execute();
    $sth->finish;
 
    my $insert = "insert into mapping (job_id, type, command_line, percent_query_cutoff, percent_target_cutoff, method, array_size) values($jobid, '$ensembl_type', '$command',".
                       $self->query_identity_threshold.", ".$self->target_identity_threshold.", '".$self->get_class_name()."', $num_jobs)";
 
 
    $sth = $mapper->xref->dbc->prepare($insert);
    $sth->execute;
    $sth->finish;
 
    $sth = $mapper->xref->dbc->prepare("insert into mapping_jobs (root_dir, map_file, status, out_file, err_file, array_number, job_id) values (?,?,?,?,?,?,?)");
    
    for( my $i=1; $i<=$num_jobs; $i++){
      my $map_file = $self->get_class_name()."_".$ensembl_type."_".$i.".map";
      my $out_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".out";
      my $err_file = "xref_0_".$ensembl_type.".".$jobid."-".$i.".err";
      $sth->execute($root_dir, $map_file, 'SUBMITTED', $out_file, $err_file, $i, $jobid);
    }
    $sth->finish;
    
  }
  
  return $unique_name;
 
}

◆ target_identity_threshold()

public XrefMapper::Methods::ExonerateBasic::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/ExonerateBasic.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ calculate_num_jobs()

◆ check_err()

◆ get_class_name()

◆ jobcount()

◆ mapper()

◆ new()

◆ options()

◆ query_identity_threshold()

◆ resubmit_exonerate()

◆ run()

◆ submit_exonerate()

◆ target_identity_threshold()