Slurping annotations

The FASTA formatted sequences can be saved from your browser as text, or copied and pasted into a text file from your browser window.
The annotations for each sequence are rendered as key=value pairs in the name line (the information line beginning with >), following the accession numbers. The following simple PERL script will convert a FASTA file as returned to an array of hashes that can be processed further. 

 # output.fas:
 # >L22956(499) 'subtype'='C' 'phenotype'='SI'
 # atgagagtgagggggatactgaggaattgtcaacaa...
 
 # use like this...
 @seqs = parse_out('output.fas');
 
 $seq[0]->{seq};          # returns 'atgagagtgagg...'
 $seq[0]->{accession};    # returns L22956
 $seq[0]->{lanl_id};      # returns 499
 $seq[0]->{phenotype};    # returns 'SI'
 $seq[0]->{subtype};      # returns 'C' 
 
 ##
 
 sub parse_out {
   my $f = shift;
   my $fh;
   open $fh, $f or die $!;
   my (@seqs, $h);
   while (<$fh>) {
     chop;
     /^>/ && do {
       $h = {};
       @a = split(/\t/);
       my $nm = shift @a;
       my $dum;
       ($dum, @{$h}{qw( accession lanl_id )}) = 
          split(/[>()]/, $nm);
       foreach my $pair (@a) {
         my ($k, $v) = split(/=/,$pair);
         $k =~ s{^'|'$}{}g;
         $v =~ s{^'|'$}{}g;
         $h->{$k} = $v;
       }
       next;
     };
     do {
       $h->{seq} = $_;
       push @seqs, $h;
     };
   }
   return @seqs;
 }
FR icon 27 Dec 2008