Re^2: PERL HTML HELP

I like the idea of having my protein sequences and the restriction enzymes displayed in various colours and i have been messing around with this but have had no luck, this is what i have tried:

 
sub color {

    my($colorkey) = @_;

    my $color = '';
    my %color_key = (
    
        A => "<font color=#99CCCC> A </font>",
        C => "<font color=#00CC00> C </font>",
        G => "<font color=#FF99CC> G </font>",
        T => "<font color=#33CC66> T </font>",
        R => "<font color=#996666> R </font>",
        Y => "<font color=#006699> Y </font>",
        M => "<font color=#33CC00> M </font>",
        K => "<font color=#99CC00> K </font>",
        S => "<font color=#000066> S </font>",
        W => "<font color=#990000> W </font>",
        B => "<font color=#0000FF> F </font>",
        D => "<font color=#FF9900> F </font>",
        H => "<font color=#9900CC> H </font>",
        V => "<font color=#99CC66> V </font>",
        N => "<font color=#33CCFF> N </font>",
        L => "<font color=#006633> L </font>",
        P => "<font color=#990066> P </font>",
        Q => "<font color=#996600> Q </font>",
        I => "<font color=#9966CC> I </font>",
        E => "<font color=#FF9966> E </font>",
        _ => "<font color=#000000> _ </font>",
    );

      # Translate each character in the sequence coloured character
    for ( my $i = 0 ; $i < length($colorkey) ; ++$i ) {
        $color
          .= $color_key{substr($colorkey, $i, 1)};
    }
    return 
}
[download]

it was a long shot but obviously did not work...trail and error eh lol either way i was wondering how would one get a key or something to store an individual amino acid as a different colour. I am assuming because the amino acid in my sequence is displayed in a string (here is my code for that):

print "please enter the start point of your DNA sequence\n\n";
$dnastart = <STDIN>;
chomp $dnastart;
print "please enter the end point of your DNA sequence\n\n";
$dnaend = <STDIN>;
chomp $dnaend;

$dna = substr($dna, $dnastart, ($dnaend - $dnastart));

print"Here is your selected DNA sequence:\n\n $dna\n\n";
}


#start the string from position 0
$protein = substr($dna,0);
#Translate the DNA to protein
$protein = dna2peptide($protein);
#Print the sequence in lines of 50 characters long
print"\n\n<----------------Peptide frame 1----------------> \n\n";
print_sequence ($protein,50); 

# printing data sequences to HTML
print OUTFILE "<table border=1 width=50% bgcolor=#CCFFFF>
<tr><td><b>  Peptide sequence frame 1</td></tr></b>
<tr></tr>
<tr><td> $protein </td></tr>
</table>";
[download]

i would need some sort of code which does a substitution for each letter into color, which is what i was trying to accomplish with my horrible attempt above lol

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Re^3: PERL HTML HELP by ww (Archbishop) on Oct 21, 2012 at 19:22 UTC
Your html still has some problems, but some are easily fixed by simply revising the quoting. Some may frown, and with reason, at this use of a 'heredoc' but it "just works" for a one-off: `#!/usr/bin/perl use 5.012; my $protein = "chuck steak"; my $heredoc = <<END <table border="1" width="50%" bgcolor="#CCFFFF"> <tr><td><b> Peptide sequence frame 1</b></td></tr>\n <tr><td>$protein </td> <td>also 'walnuts'</td></tr> </table> END ; print $heredoc;` [download] OUTPUT: `<table border="1" width="50%" bgcolor="#CCFFFF"> <tr><td><b> Peptide sequence frame 1</b></td></tr> <tr><td>chuck steak </td> <td>also 'walnuts'</td></tr> </table>` [download] Note the newline at the end of line 09; your empty `tr></tr>` will provoke complaints from some validators. Better, however, to devote a couple hours to familiarizing yourself with CSS1 and 2. And better yet to follow the broad guidance provided by blue_cowdawg ( above ) and to use such CSS constructs as "max-width: nn%" to assure that the wraps work (...err, semi-work.....) based on the user's current screen width.	[reply] [d/l] [select]

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Re^3: PERL HTML HELP
by ww (Archbishop) on Oct 21, 2012 at 19:22 UTC

heredoc

#!/usr/bin/perl
use 5.012;

my $protein = "chuck steak";

my $heredoc = <<END

<table border="1" width="50%" bgcolor="#CCFFFF">
<tr><td><b>  Peptide sequence frame 1</b></td></tr>\n
<tr><td>$protein </td> <td>also 'walnuts'</td></tr>
</table>
END
;

print $heredoc;
[download]

OUTPUT:

<table border="1" width="50%" bgcolor="#CCFFFF">
<tr><td><b>  Peptide sequence frame 1</b></td></tr>

<tr><td>chuck steak </td> <td>also 'walnuts'</td></tr>
</table>
[download]

Note the newline at the end of line 09; your empty tr></tr> will provoke complaints from some validators.

Better, however, to devote a couple hours to familiarizing yourself with CSS1 and 2. And better yet to follow the broad guidance provided by blue_cowdawg ( above ) and to use such CSS constructs as "max-width: nn%" to assure that the wraps work (...err, semi-work.....) based on the user's current screen width.

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