Finding text in a file using perl program

Question

I have a file given below:

>AAF88103.1 zinc finger protein 226 [Homo sapiens]
MNMFKEAVTFKDVAVAFTEEELGLLGPAXRKLYRDVMVENFRNLLSVGHPPFKQDVSPIERNEQLWIMTT
ATRRQGNLGEKNQSKLITVQDRESEEELSCWQIWQQIANDLTRCQDSMINNSQCHKQGDFPYQVGTELSI
QISEDENYIVNKADGPNNTGNPEFPILRTQDSWRKTFLTESQRLNRDQQISIKNKLCQCKKGVDPIGWIS
HHDGHRVHKSEKSYRPNDYEKDNMKILTFDHNSMIHTGQKSYQCNECKKPFSDLSSFDLHQQLQSGEKSL
TCVERGKGFCYSPVLPVHQKVHVGEKLKCDECGKEFSQGAHLQTHQKVHVIEKPYKCKQCGKGFSRRSAL
NVHCKVHTAEKPYNCEECGRAFSQASHLQDHQRLHTGEKPFKCDACGKSFSRNSHLQSHQRVHTGEKPYK
CEECGKGFICSSNLYIHQRVHTGEKPYKCEECGKGFSRPSSLQAHQGVHTGEKSYICTVCGKGFTLSSNL
QAHQRVHTGEKPYKCNECGKSFRRNSHYQVHLVVHTGEKPYKCEICGKGFSQSSYLQIHQKAHSIEKPFK
CEECGQGFNQSSRLQIHQLIHTGEKPYKCEECGKGFSRRADLKIHCRIHTGEKPYNCEECGKVFRQASNL
LAHQRVHSGEKPFKCEECGKSFGRSAHLQAHQKVHTGDKPYKCDECGKGFKWSLNLDMHQRVHTGEKPYK
CGECGKYFSQASSLQLHQSVHTGEKPYKCDVCGKVFSRSSQLQSHQRVHTGEKPYKCEICGKSFSWRSNL
TVHHRIHVGDKSYKSNRGGKNIRESTQEKKSIK.

In this file i am trying to look for a sequence ie: CDECGKEFSQGAHLQTHQKVH I have to hardcode this pattern in the program and then look for it, my code is as follows

    open FILE1, "file.fasta" or die;

while (my $line= <FILE1>) {

chomp $line;

}

if ($line =~ /CDECGKEFSQGAHLQTHQKVH/) {
    print "The protein contains the domain";
}else{
    print "The protein doesn't contain the domain";
}

Now this pattern occurs in the sequence but i always get the message "The protein doesn't contain the domain". Am i doing it wrong?

Answer 1

The $line evaluation occurs outside of the loop... Give this a try:

my $found = 0;
open(my $fh, '<', 'file.fasta') or die "Could not open file '$filename': $!";
while (my $line = <$fh>) {
    if ($line =~ /CDECGKEFSQGAHLQTHQKVH/) {
        $found = 1;
        last;
    }
}

if ($found == 1) {
    print "The protein contains the domain";
} else {
    print "The protein doesn't contain the domain";
}