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revision 1.414, Tue Jan 3 18:32:04 2006 UTC revision 1.415, Thu Jan 5 01:16:45 2006 UTC
# Line 8231  Line 8231 
8231   $key =~ s/\-/\_/g;   $key =~ s/\-/\_/g;
8232   $key =~ s/\W//g;   $key =~ s/\W//g;
8233   $key =~ s/\_+/\_/g;   $key =~ s/\_+/\_/g;
  unless ($old eq $key)  
  {  
   print STDERR "The key $old had illegal characters removed and is now $key. The only characters allowed in keys are [a-zA-Z0-9_]\n";  
  }  
8234   return $key;   return $key;
8235  }  }
8236    
# Line 11848  Line 11844 
11844    
11845    
11846  sub subsystems_for_genome {  sub subsystems_for_genome {
11847      my($self,$genome) = @_;      my($self,$genome, $zero) = @_;
11848    
11849      my $rdbH = $self->db_handle;      my $rdbH = $self->db_handle;
11850    
# Line 11863  Line 11859 
11859          local $dbh->{RaiseError} = 1;          local $dbh->{RaiseError} = 1;
11860          local $dbh->{PrintError} = 0;          local $dbh->{PrintError} = 0;
11861    
11862            my $sql="SELECT DISTINCT subsystem from subsystem_index WHERE (protein like 'fig\|$genome.peg.%'";
11863            unless ($zero) {$sql .= " AND (variant != '-1' AND variant != '0')"}
11864            $sql .= ")";
11865    
11866          eval {          eval {
11867              $subsystem_data = $rdbH->SQL(qq(SELECT DISTINCT subsystem from subsystem_index              $subsystem_data = $rdbH->SQL($sql);
                                             WHERE (protein like 'fig\|$genome.peg.%' AND  
                                                    variant != '-1')  
                                             ));  
11868          };          };
11869      }      }
11870    
# Line 11931  Line 11928 
11928              s/^\s*//;              s/^\s*//;
11929              s/\s*$//;              s/\s*$//;
11930              next if $_ eq "";              next if $_ eq "";
11931              if (($_ =~ /^(\d+\.\d+)\s+(\S+)/) && ($all || $2))              if (($_ =~ /^(\d+\.\d+)\s+(\S+)/) && ($all || ($2 && $2 != "-1")))
11932              {              {
11933                  my $genome = $1;                  my $genome = $1;
11934                  my $name = $self->genus_species($genome);                  my $name = $self->genus_species($genome);

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