newtoperlprog:

Something like this?

use strict;
use warnings;
use Term::ANSIColor;

my $t = "ACGCGATAGCATTAGACCTGGCACAGT";
$t =~ s/([CG]AT)/colored($1,'bold red')/ge;

print $t, "\n";
[download]

If you have the positions and lengths you want highlighted, you can do it like:

use strict;
use warnings;
use Term::ANSIColor;

my $t = "ACGCGATAGCATTAGACCTGGCACAGT";
my @highlights = (
    # [ start, len, color ]
    [ 20, 5, 'bold blue' ],
    [ 10, 2, 'bold red' ],
    [ 3, 4, 'bold green' ],
);

for my $ar (@highlights) {
    my ($start, $len, $color) = @$ar;
    $t = substr($t, 0, $start-1)                  # first part
       . colored(substr($t,$start,$len), $color)  # colored part
       . substr($t,$start+$len);                  # final part
}

print $t, "\n";
[download]

Note: If you do it this way, keep in mind that colorizing changes the positions of characters in the string, so: (1) Always start at the end and work towards the front, and (2) *NEVER* use overlapping areas.

...roboticus

When your only tool is a hammer, all problems look like your thumb.

You could start with Term::ANSIColor. Insert the ANSI-sequences for red/bold at the start of a sequence to be highlighted and switch back to normal at the end of the sequence.

I am also trying to get the output saved in a text file with the formatting of bold and red saved.

Um, bold/color? Are you talking ANSIColor or html?

color output was difficult to save in text file

You can do it. It depends of the desired output format... want a yummy pdf?

my $dna = "AAAAAACAAACAAACCCAATATATATATACGACATATATTATATATTATACCCCGGG";
my $preciouss = substr $dna, 15, 28;
 
open (my $output, '>', "latex_file.tex");

print $output "\\documentclass{article}\n\\usepackage{color}\n";
print $output "\\begin{document}\n";
print $output "THIS IS MY BORING GENE: \\textcolor{red}{", $preciouss,
+ "}\\\\\\textcolor{blue}{OKAY, OKAY... \\textit{NOT SO BORING}, {\\bf
+ IS RED!}}";
print $output "\n\\end{document}";

close $output;

system("pdflatex latex_file.tex");
system("xpdf latex_file.pdf &");
[download]

You will need to have installed a decent tex distro and xpdf. See texlive. You can also translate to html, dvi or postscript easily from here, as you will

Thank you for your reply

I have used the module Term::ANSIColor and have tried to color the output in the variable $colortext upon matching.

I am trying to keep the terminal formatting in the exported text file

Regards

What program(s) do you expect to view the exported text file in?

Colors applied with Term::ANSIColor will work with cat and less with the -R switch, but not normal text editors.

Dear Roboticus

Greatly appreciate your help. Well I tried your solution and it worked like charm. However, I am trying to do automatic array building but looks like I am not writing proper syntax.

I am trying to make the @highlights by reading a file having the position number and it doesn't seem to work, whereas if I manually put the positions in the code it the output is not as I am trying to get.

Below is my code and data:

#!/usr/bin/perl
use strict;
use warnings;
use Term::ANSIColor;
my $file = $ARGV[0];
if (@ARGV < 1){
    print STDERR "Usage: $0 input_fasta_file\n";
    exit 1;
}
my ($header, $sequence);
open (A, "<", $file) or die "Check the file: $!";
while (my $line = <A>){
    chomp $line;
    if ($line =~ /^(>.*)/){
    $header = $1;
    }
    else{
    $sequence .= $line;
    }
}
close (A);

$sequence =~s/[\n\s]//;
#print "$sequence\n";

=comment
my @highlights = (
[ 88, 1, 'bold red' ],
[ 101, 1, 'bold red' ],
[ 113, 1, 'bold red' ],
[ 121, 1, 'bold red' ],
[ 124, 1, 'bold red' ],
[ 134, 1, 'bold red' ],
[ 140, 1, 'bold red' ],
[ 146, 1, 'bold red' ],
 );
=cut

my @highlights;
my $pos_file = "sorted_position_walk.txt";
open (A, "<", $pos_file) or die "Check the file: $!";
while (my $line = <A>){
    chomp $line;
    my $pos = (split /\t/,$line)[0];
#    push(@position, $pos);
    push(@highlights, "([ $pos, 1, 'bold yellow' ],)");
}

#foreach my $pp(@highlights){
#    print "[ $pp, 1, 'bold red' ],\n";
#}

#print "@highlights\n";

for my $ar (@highlights) {
    my ($start, $len, $color) = @$ar;
    $sequence = substr($sequence, 0, $start-1)                    # fi
+rst part                               
              . colored(substr($sequence,$start,$len), $color)  # colo
+red part                           
              . substr($sequence,$start+$len);                  # fina
+l part                             
}

print $sequence, "\n";
[download]

Output with some weird characters:
TCTGTCCGCTCG3m1m[0mGGCAT
[download]

Regards

newtoperlprog:

When you use the color editing code, it inserts characters into the string. That shifts all the character positions to the right. That's why I suggested you always go from the right and work left in the note at the end. That's the reason that you're seeing weird characters in the text. Those weird characters are parts the terminal commands that tell the terminal to change colors.

For example, suppose you wanted to highlight the string CAT every time it appears, and also that the terminal command for changing the color to normal is BEER and the command to change the color to highlight is KETCHUP. Then if your input string looks like this:

ATCGCGATCATCCATACTCATTAG

Then the positions you're wanting to highlight are at 8, 12 and 18. If we apply the edits from left to right we get:

ATCGCGATBEERCATKETCHUPCCATACTCATTAG                       edit at 8
ATCGCGATBEEBEERRCAKETCHUPTKETCHUPCCATACTCATTAG            then 12
ATCGCGATBEEBEERRCABEERKETKETCHUPCHUPTKETCHUPCCATACTCATTAG then 18
        ???^^^^?  ^^^^???vvvvvvv?????vvvvvvv
[download]

UGH! The string has garbage in it now. To point it out, I've marked the resulting string with ^^^^ to indicate the command to switch to bold, vvvvvvv to show the command that switches back to normal, and ? for any garbage characters. So we'd see BEE in the regular color, followed by RCAKET in bold, then CHUPTCCATACTCATTAG in regular color. However, if we do the edits from right to left, though, we get:

ATCGCGATCATCCATACTBEERCATKETCHUPTAG                       edit at 18
ATCGCGATCATCBEERCATKETCHUPACTBEERCATKETCHUPTAG            then 12
ATCGCGATBEERCATKETCHUPCBEERCATKETCHUPACTBEERCATKETCHUPTAG then 8
        ^^^^   vvvvvvv ^^^^   vvvvvvv   ^^^^   vvvvvvv
[download]

So the three "CAT" sequences are in bold, and the rest of the string is displayed in regular color.

To convert your data to use HTML formatting instead, you can use roughly the same code, but instead of inserting BEER and KETCHUP from Term::ANSIColor (or whatever it is that it uses for your terminal), you could use <font color="red"> and </font> as Anonymous Monk indicated later in the thread. In that case, though, you'll *still* want to go from right to left!

Notes:

1) Now that the node is formatted, I'm really revolted by the pairing of beer and ketchup. But it was annoying enough to format that I'll leave it alone, nausea-inducing as it is.

2) If you had replied to my node instead of yourself, I'd've seen the message sooner and replied. (When time pressed, I generally only look at top-level nodes and replies to my nodes.)

...roboticus

When your only tool is a hammer, all problems look like your thumb.

Dear Roboticus and Anonymous Monk

Thank you for your suggestions and directions and I am extremely sorry for any confusion if any.

As you mentioned in your earlier post, that this will not work if the sequences are overlapping and I have found that some of my regions would be overlapping.

I was also thinking if this could be done by an array of range operator and for each array element the sequence will be either bold or colored.

Below is my code which I was trying:

#!/usr/bin/perl
#use strict;
use warnings;

my $filename =  "NM_014143.3.fasta";
my @name     = split( /\./, $filename );
my $name     = $name[0];
my ($infile, @temp);
open( $infile, "<", $filename ) || die "Check the $filename $!\n";
while ( my $line = <$infile> ) 
{
    chomp $line;
    if    ( $line =~ /^>/ )    { next; }
    elsif ( $line =~ /^\s*$/ ) { next; }
    elsif ( $line =~ /^\s*#/ ) { next; }
    else                       { $sequence .= $line; }
}
$sequence =~ s/\n//g;
$sequence =~ s/\s+//g;
#print "$sequence\n";
close ($infile);

my @seq = (1 .. 15, 30 .. 40, 50 .. 60); #this is a range array

for (my $pos=1;$pos<=length($sequence);$pos++){
    foreach my $ar(@seq){
    if($pos == $ar){
        push (@temp, "<b>",$sequence, "</b");
    }
    else{
        push (@temp, $sequence);
    }
    }
}
my $tmp = join ("", @temp);
print "$tmp\n";
[download]

Data file:
GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACC
+                                                                   CC
+TGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGACCATTTGCTGAACGCATT
TACTGTCACGGTTCCCAAGGACCTATATGTGGTAGAGTATGGTAGC                        
+                                                                   AT
+GACAATTGAATGCAAATTCCCAGTAGAAAAACAATTAGACCTGGCTGCACTAATTGTCTATTGGG
AAATGGAGGATAAGAACATTATTCAATTTGTGCATGGAGAGGAAGACCTGAAGGTTCAGCATAGTAGCTA
CAGACAGAGGGCCCGGCTGTTGAAGGACCAGCTCTCCCTGGGAAATGCTGCACTTCAGATCACAGATGTG
AAATTGCAGGATGCAGGGGTGTACCGCTGCATGATCAGCTATGGTGGTGCCGACTACAAGCGAATTACTG
TGAAAGTCAATGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACA
TGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTC
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA
[download]

Dear All

Thank you for your replies

Since, color output was difficult to save in text file. I am now trying to make the output as html formatted which will suffice my need.

For the sequence file, I am trying to color the font red for a part of sequence, leaving rest as default font color (black).

 
#!/usr/bin/perl                                                       
+              
use strict;
use warnings;

my $sequence = '';
my $filename =  "NM_014143.3.fasta";
my @name     = split( /\./, $filename );
my $name     = $name[0];
my $infile;
my $outfile;my $out;my $reject; my @missing;
open( $infile, "<", $filename ) || die "Check the $filename $!\n";

while ( my $line = <$infile> )
{
    chomp $line;
    if    ( $line =~ /^>/ )    { next; }
    elsif ( $line =~ /^\s*$/ ) { next; }
    elsif ( $line =~ /^\s*#/ ) { next; }
    else                       { $sequence .= $line; }
}
$sequence =~ s/\n//g;
$sequence =~ s/\s+//g;
#print "$sequence\n";                                                 
+              
close ($infile);

my @seq = (1 .. 15, 30 .. 40, 50 .. 60);

for (my $pos = 0; $pos <= length($sequence); $pos++){
    foreach my $ran (@seq){
        my $frag = substr($sequence, $pos, $ran);
        print "<font color=\"red\">$frag</font>\n";
    }
}
[download]

 Data file:
>gi|292658763|ref|NM_014143.3| Homo sapiens CD274 molecule (CD274), tr
+anscript variant 1, mRNA
GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACC
AGCCGCGCTTCTGTCCGCCTGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGAC
CTACTGGCATTTGCTGAACGCATTTACTGTCACGGTTCCCAAGGACCTATATGTGGTAGAGTATGGTAGC
AATATGACAATTGAATGCAAATTCCCAGTAGAAAAACAATTAGACCTGGCTGCACTAATTGTCTATTGGG
AAATGGAGGATAAGAACATTATTCAATTTGTGCATGGAGAGGAAGACCTGAAGGTTCAGCATAGTAGCTA
CAGACAGAGGGCCCGGCTGTTGAAGGACCAGCTCTCCCTGGGAAATGCTGCACTTCAGATCACAGATGTG
AAATTGCAGGATGCAGGGGTGTACCGCTGCATGATCAGCTATGGTGGTGCCGACTACAAGCGAATTACTG
TGAAAGTCAATGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACA
TGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTC
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA
GAATCAACACAACAACTAATGAGATTTTCTACTGCACTTTTAGGAGATTAGATCCTGAGGAAAACCATAC
[download]

The problem I am facing is how to print the sequence with selected regions as red font color.

 Desired output:
<font color="red">GGCGCAACGCTGAGC</font>AGCTGGCGCGTCCCG<font color="re
+d">CGCGGCCCCA</font>GTTCTGCGCA<font color="red">GCTTCCCGAG</font>GCTC
+CGCACC
AGCCGCGCTTCTGTCCGCCTGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGAC
CTACTGGCATTTGCTGAACGCATTTACTGTCACGGTTCCCAAGGACCTATATGTGGTAGAGTATGGTAGC
AATATGACAATTGAATGCAAATTCCCAGTAGAAAAACAATTAGACCTGGCTGCACTAATTGTCTATTGGG
AAATGGAGGATAAGAACATTATTCAATTTGTGCATGGAGAGGAAGACCTGAAGGTTCAGCATAGTAGCTA
CAGACAGAGGGCCCGGCTGTTGAAGGACCAGCTCTCCCTGGGAAATGCTGCACTTCAGATCACAGATGTG
AAATTGCAGGATGCAGGGGTGTACCGCTGCATGATCAGCTATGGTGGTGCCGACTACAAGCGAATTACTG
TGAAAGTCAATGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACA
TGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTC
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA
GAATCAACACAACAACTAATGAGATTTTCTACTGCACTTTTAGGAGATTAGATCCTGAGGAAAACCATAC
[download]

Thank you and any help will be greatly appreciated.

Regards

roboticus's suggestion can easily be adapted to output HTML (why did you stop using it when it "worked like charm"?). Simply replace the part that calls the colored function with your "<font ..." strings. Keep in mind roboticus's comment that the positions for replacements need to be in descending order, so you may want to sort your array of positions accordingly.