Dear All

I am trying to output a sequence file with some region bold and colored red using perl script.

Below is my script and files

 
#!/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]//;
my @sequence = split ("", $sequence);
#print "@sequence\n";

my @position;
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);
}

for (my $i=0;$i<=scalar(@sequence);$i++){
    foreach my $value(@position){
    if($value eq $sequence[$i]){
        my $colortext = colored (($value+18), 'bold red');
        print "$sequence[$i]\n";
    }
    }
}

[download]
Fasta 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
AGCTGAATTGGTCATCCCAGAACTACCTCTGGCACATCCTCCAAATGAAAGGACTCACTTGGTAATTCTG
GGAGCCATCTTATTATGCCTTGGTGTAGCACTGACATTCATCTTCCGTTTAAGAAAAGGGAGAATGATGG
ATGTGAAAAAATGTGGCATCCAAGATACAAACTCAAAGAAGCAAAGTGATACACATTTGGAGGAGACGTA
ATCCAGCATTGGAACTTCTGATCTTCAAGCAGGGATTCTCAACCTGTGGTTTAGGGGTTCATCGGGGCTG
AGCGTGACAAGAGGAAGGAATGGGCCCGTGGGATGCAGGCAATGTGGGACTTAAAAGGCCCAAGCACTGA
AAATGGAACCTGGCGAAAGCAGAGGAGGAGAATGAAGAAAGATGGAGTCAAACAGGGAGCCTGGAGGGAG
ACCTTGATACTTTCAAATGCCTGAGGGGCTCATCGACGCCTGTGACAGGGAGAAAGGATACTTCTGAACA
AGGAGCCTCCAAGCAAATCATCCATTGCTCATCCTAGGAAGACGGGTTGAGAATCCCTAATTTGAGGGTC
AGTTCCTGCAGAAGTGCCCTTTGCCTCCACTCAATGCCTCAATTTGTTTTCTGCATGACTGAGAGTCTCA
GTGTTGGAACGGGACAGTATTTATGTATGAGTTTTTCCTATTTATTTTGAGTCTGTGAGGTCTTCTTGTC
ATGTGAGTGTGGTTGTGAATGATTTCTTTTGAAGATATATTGTAGTAGATGTTACAATTTTGTCGCCAAA
CTAAACTTGCTGCTTAATGATTTGCTCACATCTAGTAAAACATGGAGTATTTGTAAGGTGCTTGGTCTCC
TCTATAACTACAAGTATACATTGGAAGCATAAAGATCAAACCGTTGGTTGCATAGGATGTCACCTTTATT
TAACCCATTAATACTCTGGTTGACCTAATCTTATTCTCAGACCTCAAGTGTCTGTGCAGTATCTGTTCCA
TTTAAATATCAGCTTTACAATTATGTGGTAGCCTACACACATAATCTCATTTCATCGCTGTAACCACCCT
GTTGTGATAACCACTATTATTTTACCCATCGTACAGCTGAGGAAGCAAACAGATTAAGTAACTTGCCCAA
ACCAGTAAATAGCAGACCTCAGACTGCCACCCACTGTCCTTTTATAATACAATTTACAGCTATATTTTAC
TTTAAGCAATTCTTTTATTCAAAAACCATTTATTAAGTGCCCTTGCAATATCAATCGCTGTGCCAGGCAT
TGAATCTACAGATGTGAGCAAGACAAAGTACCTGTCCTCAAGGAGCTCATAGTATAATGAGGAGATTAAC
AAGAAAATGTATTATTACAATTTAGTCCAGTGTCATAGCATAAGGATGATGCGAGGGGAAAACCCGAGCA
GTGTTGCCAAGAGGAGGAAATAGGCCAATGTGGTCTGGGACGGTTGGATATACTTAAACATCTTAATAAT
CAGAGTAATTTTCATTTACAAAGAGAGGTCGGTACTTAAAATAACCCTGAAAAATAACACTGGAATTCCT

[download]
Sorted_position_walk.txt
88
91
92
94
101
113
114
121
122
124
125
126
134
140
146
148
153
159
171
173
183

[download]

The final output I am trying to get is to bold and red for the regions which matches the sorted_position_walk.txt file (match number + 18) so total of 19 characters bold and red. For exapmple, in the final output the sequence should have regions from position number 88 +18 as bold and red and so on.

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

Any help and direction will be greatly appreciated.

Regards

In reply to bold color text and export to file by newtoperlprog

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