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revision 1.2, Sun Dec 13 01:11:40 2009 UTC revision 1.3, Mon Dec 28 21:34:23 2009 UTC
# Line 99  Line 99 
99      my($role) = @_;      my($role) = @_;
100    
101      my %figfams;      my %figfams;
102      foreach $_ (`cat /Users/rossoverbeek/FIGdisk/FIG/Data/FigfamsData/family.functions`)      foreach $_ (`cat $FIG_Config::FigfamsData/family.functions`)
103      {      {
104          if ((index($_,$role) >= 0) && ($_ =~ /^(FIG\d{6})/))          if ((index($_,$role) >= 0) && ($_ =~ /^(FIG\d{6})/))
105          {          {
# Line 110  Line 110 
110      my $genomesH  = $sapO->all_genomes(-complete => 1);      my $genomesH  = $sapO->all_genomes(-complete => 1);
111      my @ids =  grep { $genomesH->{&SeedUtils::genome_of($_)} }      my @ids =  grep { $genomesH->{&SeedUtils::genome_of($_)} }
112                 map { (($_ =~ /^(\S+)\t(\S+)/) && $figfams{$1}) ? $2 : () }                 map { (($_ =~ /^(\S+)\t(\S+)/) && $figfams{$1}) ? $2 : () }
113                `cat /Users/rossoverbeek/FIGdisk/FIG/Data/FigfamsData/families.2c`;                `cat $FIG_Config::FigfamsData/families.2c`;
114      my $idsH = $sapO->ids_to_sequences(-ids => \@ids, -protein => 1);      my $idsH = $sapO->ids_to_sequences(-ids => \@ids, -protein => 1);
115      return [map { my $seq = $idsH->{$_}; $seq ? [$_,'',$seq] : () } keys(%$idsH)];      return [map { my $seq = $idsH->{$_}; $seq ? [$_,'',$seq] : () } keys(%$idsH)];
116  }  }

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