edwardslab

The following perl subroutine will read in a fasta formatted file, parse the file, and return all the sequences in a reference to a hash table.

sub get_fasta{
  open(FILE, "<@_") or die("Cannot open FASTA file.\n");
  my %seqs;
  my $header; 
  my $first = 0;
  my @lines = ;
  foreach my $line(@lines){
  chomp($line);
  if ($line =~ /^>/){
    $header = $line;
    $header =~ s/^>//;
    $header =~ s/\s.*//;
    if ($first == 0){
      $first = 1;
    }
    next;
  }
  if ($first == 0){ die("Not a standard FASTA file.\n"); }
    $seqs{$header} = $seqs{$header}.$line;
  }
  close(FILE);
  return \%seqs;
}

my $seqs = &get_fasta("filename.txt");
  foreach(keys %$seqs){
    print $_;
    print $$seqs{$_},"\n"; 
  }
}