simplify fasta parser and add support for gzipped fasta input

lib/FastaDatabase.pm

@@ -59,26 +59,19 @@ sub from_fasta {
     my $seqdata = {};
 
     for my $filename ( @files ) {
-        my $sep = $/;
-        local *FILE;
-        open FILE, "<$filename" or die "Couldn't open '$filename': $!";
-
-        $/ = ">";
-        my $dummy = <FILE>;
-        my $name;
-        while (($/ = "\n", $name = <FILE>)[1]) {
-            chomp $name;
-            $name =~ s/^\s*(\S+).*$/$1/; # throw away description metadata after name
-            $/ = ">";
-            my $seq = <FILE>;
-            chomp $seq;
-            $/ = $sep;
+
+	my $gzip = $filename =~ /\.gz(ip)?$/i ? ':gzip' : '';
+
+        open my $fh, "<$gzip", $filename or die "Couldn't open '$filename': $!";
+
+        local $/ = "\n>";
+        while( my $entry = <$fh> ) {
+            chomp $entry;
+	    my ( $name, $seq ) = split "\n", $entry, 2;
+	    ($name) = $name =~ s/^\s*>\s*(\S+)//;
             $seq =~ s/\s//g;
             $seqdata->{$name} = $seq;
         }
-
-        close FILE;
-        $/ = $sep;
     }
 
     my $self = $class->new ('seqdata' => $seqdata);