Re: perlkhan 77

[apl]

In addition to the earlier comments, I'd suggest changing (as an example)

  $count_G = ( $seq =~ tr/G//);
  $ratio_G = ($count_G/$len);
# print "\n$ratio_G\n";

to

  $ratio_G = Calculate( 'G' );

Writing the sub Calculate is left as an exercise to the reader. The advantages are you

• get rid of all of the temporary $count_* variables
• remove duplicated code
• make future changes (e.g. you want percentage rather than ratio) more centralized
• make the intentions of your code much clearer

[Anonymous Monk]

sub Passref {
    my ( $define, $seq, $count, $outfh ) = @_;
    chomp($define);
    my $len   = length($$seq);
    my %count = ( Miss => 0+( $$seq =~ m/^YCWLPHQIMTNKSRVADEGF/ig ) );
    # YCWLPHQIMTNKSRVADEGF doesn't appear in test file
    my %ratio = ( Miss => 0+( $count{Miss} / $len ) );
    for my $letter (qw[ E D A V R S K N T M I Q H P L W C Y F ]) {
        $count{$letter} = ( $$seq =~ m/$letter/g );
        $ratio{$letter} = $count{$letter} / $len;
    }
    print {$outfh} join "\t", $define, $len,
      @ratio{qw[ E D A V R S K N T M I Q H P L W C Y F Miss  ]}, "\n";
}

[Anonymous Monk]

For count you need

$count{$letter} = ()= $$seq =~ m/$letter/g;