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revision 1.2, Tue Apr 10 20:40:57 2007 UTC revision 1.3, Tue Apr 10 20:51:36 2007 UTC
# Line 40  Line 40 
40  my $job = new Job48($job_id);  my $job = new Job48($job_id);
41    
42  my $meta = $job->meta;  my $meta = $job->meta;
43    my $genome = $job->genome_id();
44    
45  print "Running job! $jobdir\n";  print "Running job! $jobdir\n";
46    
# Line 59  Line 60 
60  #  #
61  sub create_seed_gff  sub create_seed_gff
62  {  {
     my $genome = $job->genome_id();  
63    
64      #      #
65      # consolidate all the blastx generated sims into a single file      # consolidate all the blastx generated sims into a single file
# Line 221  Line 221 
221  #  #
222  sub process_rdp  sub process_rdp
223  {  {
224        my $orgdir = "$jobdir/rp/$genome";
225    
226      for my $name (qw(16s gg lsu ssu))      for my $name (qw(16s gg lsu ssu))
227      {      {
228          my $dir = "$jobdir/proc/sims.$name";          my $dir = "$jobdir/proc/sims.$name";
# Line 231  Line 233 
233          # Now we can invoke the appropriate analysis.          # Now we can invoke the appropriate analysis.
234          #          #
235    
236            my $besthits = "$orgdir/taxa.$name.besthits";
237            my $allhits =  "$orgdir/taxa.$name.allhits";
238    
239          if ($name eq 'gg')          if ($name eq 'gg')
240          {          {
241              my @cmd = ("$FIG_Config::bin/blast2taxa", $sims, "$sims.besthits", "$sims.allhits");              my @cmd = ("$FIG_Config::bin/blast2taxa", $sims, $besthits, $allhits);
242              my $rc = system(@cmd);              my $rc = system(@cmd);
243              if ($rc != 0)              if ($rc != 0)
244              {              {
# Line 250  Line 255 
255                         '-b', $sims,                         '-b', $sims,
256                         '-c', '1e-5',                         '-c', '1e-5',
257                         '-l', '50',                         '-l', '50',
258                         '-ah', "$sims.allhits",                         '-ah', $allhits,
259                         '-bh', "$sims.besthits");                         '-bh', $besthits);
260              print "Run @cmd\n";              print "Run @cmd\n";
261              my $rc = system(@cmd);              my $rc = system(@cmd);
262              if ($rc != 0)              if ($rc != 0)

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