Re: perlkhan 77

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";
[download]

  $ratio_G = Calculate( 'G' );
[download]

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

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Re^2: perlkhan 77 by Anonymous Monk on Apr 22, 2009 at 12:10 UTC
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} = ( $$seq =~ m/$letter/g ); $ratio{$letter} = $count{$letter} / $len; } print {$outfh} join "\t", $define, $len, @ratio{qw[ E D A V R S K N T M I Q H P L W C Y F Miss ]}, "\n"; } [download]	[reply] [d/l]
Re^3: perlkhan 77 by Anonymous Monk on Apr 22, 2009 at 12:34 UTC
For count you need `$count{$letter} = ()= $$seq =~ m/$letter/g;` [download]	[reply] [d/l]