Base class with most of exonerate functionality and overridable methods

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm

+# Base class that all other mapping methods inherit from
+
+package XrefMapper::Methods::ExonerateBasic;
+
+use strict;
+
+use File::Basename;
+use IPC::Open3;
+
+# Path to exonerate executable
+my $exonerate_path = "/usr/local/ensembl/bin/exonerate-0.8.3";
+
+
+sub new {
+
+  my($class) = @_;
+
+  my $self ={};
+  bless $self,$class;
+
+  return $self;
+
+}
+
+=head2 run
+
+  Arg[1]     : Query filename to pass to exonerate; this should be the XREF file.
+  Arg[2]     : Target filename to pass to exonerate; this should be the ENSEMBL file.
+  Example    : none
+  Description: Run exonerate with default options.
+  Returntype : none
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub run() {
+
+  my ($self, $query, $target) = @_;
+
+  my $name = $self->submit_exonerate($query, $target, options());
+
+  return $name;
+
+}
+
+=head2 options
+
+  Args       : none
+  Example    : none
+  Description: Options to pass to exonerate. Override as appropriate.
+  Returntype : List of strings.
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub options() {
+
+  return ();
+
+}
+
+=head2 submit_exonerate
+
+  Args       : none
+  Example    : none
+  Description: Submit a *single* mapping job array to exonerate.
+  Returntype : The name of the job array submitted to LSF. Can be used in depend job.
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub submit_exonerate {
+
+  my ($self, $query, $target, @options) = @_;
+
+  my $num_jobs = calculate_num_jobs($query);
+
+  # TODO - get root_dir from config
+  my $root_dir = "/nfs/acari/gp1/work/ensembl/misc-scripts/xref_mapping";
+
+  my $options_str = join(" ", @options);
+
+  my $unique_name = $self->get_class_name() . "_" . time();
+
+  my $prefix = $root_dir . "/" . basename($query);
+  $prefix =~ s/\.\w+$//;
+
+  my $output = $self->get_class_name() . "_\$LSB_JOBINDEX.map";
+
+  my @main_bsub = ( 'bsub', '-J', $unique_name . "[1-$num_jobs]", '-o', "$prefix.%I.out", '-e', "$prefix.%I.err");
+
+  #print "bsub command: " . join(" ", @main_bsub) . "\n\n";
+
+  # Use IPC::Open3 to open the process so that we can read and write from/to its stdout/stderr
+  my ($wtr, $rtr, $etr, $pid);
+  $pid = open3($wtr, $rtr, $etr, @main_bsub);
+
+  # Create actual execute script to be executed with LSF, and write to pipe
+  my $main_job = <<EOF;
+. /usr/local/lsf/conf/profile.lsf
+
+cd /tmp
+
+rm -f /tmp/\$LSB_JOBINDEX.$query /tmp/\$LSB_JOBINDEX.$target /tmp/$output
+
+lsrcp ecs1a:$root_dir/$target /tmp/\$LSB_JOBINDEX.$target
+lsrcp ecs1a:$root_dir/$query  /tmp/\$LSB_JOBINDEX.$query
+
+$exonerate_path /tmp/\$LSB_JOBINDEX.$query /tmp/\$LSB_JOBINDEX.$target --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%qab:%qae:%tab:%tae:%C:%s\n" $options_str | grep '^xref' > /tmp/$output
+
+lsrcp /tmp/$output ecs1a:$root_dir/$output
+
+rm -f /tmp/\$LSB_JOBINDEX.$query /tmp/\$LSB_JOBINDEX.$target /tmp/$output
+EOF
+
+  # TODO make sure query/target are the right way round
+
+  print $wtr $main_job;
+
+  #print "Job:\n" . $main_job . "\n\n";
+
+  close($wtr);
+
+  # Wait until bsub has actually run - will print to its stdout ($rtr) and then close it
+  my $jobid;
+  while (<$rtr>) {
+    if (/Job <([0-9]+)> is/) {
+      $jobid = $1;
+      print "LSF job ID for main mapping job: $jobid \n"
+    }
+  }
+  if (!defined($jobid)) {
+    print STDERR "Error: could not get LSF job ID for mapping job\n";
+  }
+
+  return $unique_name;
+
+}
+
+=head2 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
+
+=cut
+
+sub calculate_num_jobs {
+
+  my $query = shift;
+
+  my $bytes_per_job = 250000;
+
+  my $size = (stat $query)[7];
+
+  return int($size/$bytes_per_job);
+
+}
+
+# Get class name from fully-qualified object name
+# e.g. return ExonerateBasic from XrefMapper::Methods::ExonerateBasic=HASH(Ox12113c0)
+
+sub get_class_name() {
+
+  my $self = shift;
+
+  $self =~ s/=.*$//;
+
+  my @bits = split(/::/, $self);
+
+  return @bits[$#bits];
+
+}
+
+1;
+