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