Thanks for your answers. I would like to thank Daveorg for his explanation and highlighting my problem. I'm still having some problem in solving my problem. I have sent the structure of the file am dealing with and the code I have so far come up with using a REGEX that captures only the first line in the file.

The structure of the text file is as follows:

FT CDS complement(7216..17805)
FT /locus_tag="TP01_0003"
FT /codon_start=1
FT /protein_id="XP_765530.1"
FT /db_xref="GI:71031777"
FT /db_xref="GeneID:3502673"
FT gene complement(<7216..>17805)
FT /locus_tag="TP01_0003"
FT /db_xref="GeneID:3502673"
FT mRNA complement(<7216..>17805)
FT /locus_tag="TP01_0003"
FT /product="hypothetical telomeric SfiI fragment 20 protein
FT 3"
FT /transcript_id="XM_760437.1"
FT /db_xref="GI:71031776"
FT /db_xref="GeneID:3502673"
FT CDS complement(join(18028..18116,19351..20668))
FT /locus_tag="TP01_0004"
FT /note="go_function: nutrient reservoir activity [goid
FT 0045735]"
FT /codon_start=1
FT /protein_id="XP_765531.1"
FT /db_xref="GI:71031779"
FT /db_xref="GeneID:3503550"
FT gene complement(<18028..>20668)
FT /locus_tag="TP01_0004"
FT /db_xref="GeneID:3503550"
FT mRNA complement(join(<18028..18116,19351..>20668))
FT /locus_tag="TP01_0004"
FT /product="hypothetical protein"
FT /transcript_id="XM_760438.1"
FT /db_xref="GI:71031778"
FT /db_xref="GeneID:3503550"
FT CDS complement(20951..21967)
FT /locus_tag="TP01_0005"
FT /codon_start=1
FT /protein_id="XP_765532.1"
FT /db_xref="GI:71031781"
FT /db_xref="GeneID:3503551"
FT gene complement(<20951..>21967)
FT /locus_tag="TP01_0005"
FT /db_xref="GeneID:3503551"
FT mRNA complement(<20951..>21967)
FT /locus_tag="TP01_0005"
FT /product="hypothetical protein"
FT /transcript_id="XM_760439.1"
FT /db_xref="GI:71031780"
FT /db_xref="GeneID:3503551"
[download]

This is my code

#!/usr/bin/perl
$file = 'Muguga.embl ';

open (F, $file) || die ("Could not open $file!");

while ($line = <F>)
{
($field1,$field2,$field3,$field4) = split( "\t" , $line);

print "$field1 $field2 $field3 $field4 \n";
my $string = (FT CDS complement(join(18028..18116,19351..20668))); # s
+tring to be searched

if ($string = ~ m/^FT \s+ CDS \s+ complement\(join\([0-9]+\)\)$/)
#search for the first line highlighted in bold
{
print 'match'
} else{
print 'no match';
}
}
close (F);
[download]

My wish is to able to search for the lines that are in bold and print them out.

I will be grateful if you are able to help my code though am still a perl newbie.

Thanks in advance.

20090716 Janitored by Corion: Added formatting, code tags, as per Writeup Formatting Tips