Question

I am using perl to search for a specific strings in a file with different sequences listed under different headings. I am able to write script when there is one sequence present i.e one heading but am not able to extrapolate it.
suppose I am reqd to search for some string “FSFSD” in a given file then eg:
can’t search if file has following content :

Polons
CACAGTGCTACGATCGATCGATDDASD
HCAYCHAYCHAYCAYCSDHADASDSADASD
Seliems
FJDSKLFJSLKFJKASFJLAKJDSADAK
DASDNJASDKJASDJDSDJHAJDASDASDASDSAD
Teerag
DFAKJASKDJASKDJADJLLKJ
SADSKADJALKDJSKJDLJKLK

Can search when file has one heading i.e:

Terrans
FDKFJSKFJKSAFJALKFJLLJ
DKDJKASJDKSADJALKJLJKL
DJKSAFDHAKJFHAFHFJHAJJ

I need to output the result as “String xyz found under Heading abc”

The code I am using is:

print "Input the file name \n";
$protein= <STDIN>;
chomp $protein;
unless (open (protein, $protein))
{
print "cant open file \n\n";
exit;
}
@prot= <protein>;
close protein;
$newprotein=join("",@prot);
$protein=~s/\s//g;
do{
print "enter the motif to be searched \n";
$motif= <STDIN>;
chomp $motif;
if ($protein =~ /motif/)
{
print "found motif \n\n";
}
else{
print "not found \n\n";
}
}
until ($motif=~/^\s*$/);
exit;

Answer 1

The main issue is how do you distinguish between a header and the data, from your examples I assume that a line is a header iff it contains a lower case letter.

use strict;
use warnings;
print "Enter the motif to be searched \n";
my $motif = <STDIN>;
chomp($motif);
my $header;
while (<>) {
    if(/[a-z]/) {
        $header = $_;
        next;
    }
    if (/$motif/o) {
        print "Found $motif under header $header\n";
        exit;
    }
}
print "$motif not found\n";