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revision 1.1, Sun Dec 13 01:02:49 2009 UTC revision 1.2, Sun Dec 13 01:11:40 2009 UTC
# Line 29  Line 29 
29  my @reference = sort { $counts{$b} <=> $counts{$a} } keys(%counts);  my @reference = sort { $counts{$b} <=> $counts{$a} } keys(%counts);
30  if (@reference > 30) { $#reference = 29 }  if (@reference > 30) { $#reference = 29 }
31    
32    my $sapO = SAPserver->new;
33  my $genomesH  = $sapO->all_genomes(-complete => 1);  my $genomesH  = $sapO->all_genomes(-complete => 1);
34  open(CLOSE,">$gdir/closest.genomes") || die "could not open closest.genomes";  open(CLOSE,">$gdir/closest.genomes") || die "could not open closest.genomes";
35  foreach my $g2 (@reference)  foreach my $g2 (@reference)
# Line 110  Line 111 
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 /Users/rossoverbeek/FIGdisk/FIG/Data/FigfamsData/families.2c`;
     my $sapO = SAPserver->new;  
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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