$type ||= Maasha::Seq::seq_guess_type( $entry1->[ SEQ ] );
- $blosum = blosum_read() if $type =~ /protein/;
+ $blosum = blosum_read() if $type =~ "PROTEIN";
for ( $i = 0; $i < length $entry1->[ SEQ ]; $i++ )
{
- $char1 = substr $entry1->[ SEQ ], $i, 1;
- $char2 = substr $entry2->[ SEQ ], $i, 1;
+ $char1 = uc substr $entry1->[ SEQ ], $i, 1;
+ $char2 = uc substr $entry2->[ SEQ ], $i, 1;
if ( $blosum and $char1 eq $char2 ) {
$pins .= $char1;
- } elsif ( uc $char1 eq uc $char2 ) {
+ } elsif ( $char1 eq $char2 ) {
$pins .= "|";
- } elsif ( $blosum and $blosum->{ $char1 }->{ $char2 } > 0 ) {
+ } elsif ( $blosum and defined $blosum->{ $char1 }->{ $char2 } and $blosum->{ $char1 }->{ $char2 } > 0 ) {
$pins .= "+";
} else {
$pins .= " ";
$type = Maasha::Seq::seq_guess_type( $seq1 );
- if ( $type =~ /rna/i ) {
+ if ( $type eq "RNA" ) {
$seq2 = Maasha::Seq::rna_revcomp( $seq1 );
- } elsif ( $type =~ /dna/i ) {
+ } elsif ( $type eq "DNA" ) {
$seq2 = Maasha::Seq::dna_revcomp( $seq1 );
} else {
Maasha::Common::error( qq(Bad sequence type->$type) );