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revision 1.29, Wed Mar 31 16:32:22 2004 UTC revision 1.30, Wed Mar 31 18:39:15 2004 UTC
# Line 393  Line 393 
393          foreach $x (@annotations)          foreach $x (@annotations)
394          {          {
395              $peg = $x->[0];              $peg = $x->[0];
396              my @aliases = grep { $_ =~ /^(sp\||gi\||pirnr\||kegg\||N[PGZ]_)/ } $self->feature_aliases($peg);              my @aliases = grep { $_ =~ /^(sp\||gi\||pirnr\||kegg\||N[PGZ]_)/ } $fig->feature_aliases($peg);
397              print ANNOTATIONS join("\t",($peg,join(",",@aliases),$self->genus_species($self->genome_of($peg)),scalar $self->function_of($peg))) . "\n";              print ANNOTATIONS join("\t",($peg,join(",",@aliases),$fig->genus_species($fig->genome_of($peg)),scalar $fig->function_of($peg))) . "\n";
398          }          }
399          print ANNOTATIONS "//\n";          print ANNOTATIONS "//\n";
400    
401          foreach $x (@annotations)          foreach $x (@annotations)
402          {          {
403              ($peg,undef) = @$x;              ($peg,undef) = @$x;
404              my $seq = $self->get_translation($peg);              my $seq = $fig->get_translation($peg);
405              &FIG::display_id_and_seq($peg,\$seq,\*ANNOTATIONS);              &FIG::display_id_and_seq($peg,\$seq,\*ANNOTATIONS);
406          }          }
407          close(ANNOTATIONS);          close(ANNOTATIONS);
# Line 580  Line 580 
580          foreach $x (@assignments)          foreach $x (@assignments)
581          {          {
582              ($peg,undef) = @$x;              ($peg,undef) = @$x;
583              my @aliases = grep { $_ =~ /^(sp\||gi\||pirnr\||kegg\||N[PGZ]_)/ } $self->feature_aliases($peg);              my @aliases = grep { $_ =~ /^(sp\||gi\||pirnr\||kegg\||N[PGZ]_)/ } $fig->feature_aliases($peg);
584              print ASSIGNMENTS join("\t",($peg,join(",",@aliases),$self->genus_species($self->genome_of($peg)),scalar $self->function_of($peg))) . "\n";              print ASSIGNMENTS join("\t",($peg,join(",",@aliases),$fig->genus_species($fig->genome_of($peg)),scalar $fig->function_of($peg))) . "\n";
585          }          }
586          print ASSIGNMENTS "//\n";          print ASSIGNMENTS "//\n";
587    
588          foreach $x (@assignments)          foreach $x (@assignments)
589          {          {
590              ($peg,undef) = @$x;              ($peg,undef) = @$x;
591              my $seq = $self->get_translation($peg);              my $seq = $fig->get_translation($peg);
592              &FIG::display_id_and_seq($peg,\$seq,\*ASSIGNMENTS);              &FIG::display_id_and_seq($peg,\$seq,\*ASSIGNMENTS);
593          }          }
594          close(ASSIGNMENTS);          close(ASSIGNMENTS);
# Line 618  Line 618 
618      $userR = $user;      $userR = $user;
619      $userR =~ s/^master://;      $userR =~ s/^master://;
620    
621      while (defined($line = <IN>) && ($line !~ /^\/\./))      while (defined($line = <IN>) && ($line !~ /^\/\//))
622      {      {
623          if ($line =~ /^(fig\|\d+\.\d+\.peg\.\d+)\t(\S.*\S)/)          if ($line =~ /^(fig\|\d+\.\d+\.peg\.\d+)\t(\S.*\S)/)
624          {          {
# Line 688  Line 688 
688  sub package_translation_rules {  sub package_translation_rules {
689      my($fig_base,$file) = @_;      my($fig_base,$file) = @_;
690    
     &force_absolute($fig_base);  
     &force_absolute($file);  
691      &FIG::run("cp $fig_base/Data/Global/function.synonyms $file");      &FIG::run("cp $fig_base/Data/Global/function.synonyms $file");
692  }  }
693    
# Line 747  Line 745 
745  }  }
746    
747  sub package_subsystems {  sub package_subsystems {
748      my($file,$just_exchangable) = @_;      my($fig,$file,$just_exchangable) = @_;
749      my($ssa);      my($ssa);
750    
751      $just_exchangable = defined($just_exchangable) ? $just_exchangable : 1;      $just_exchangable = defined($just_exchangable) ? $just_exchangable : 1;
# Line 771  Line 769 
769      }      }
770  }  }
771    
772    sub install_subsystems {
773        my($fig,$package) = @_;
774    
775        &FIG::run("import_subsystems master last_release < $package");
776    }
777    
778  1  1

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