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 i.e: 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?

Crossposted to PerlMonks.

choroba
– choroba

2020-04-14 14:24:22 +00:00
Commented Apr 14, 2020 at 14:24 — choroba
– choroba, Commented Apr 14, 2020 at 14:24

Toto · Accepted Answer · 2020-04-14 10:16:36Z

3

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";
}

edited Apr 14, 2020 at 10:16

Toto

91.7k63 gold badges97 silver badges135 bronze badges

answered Apr 14, 2020 at 6:27

James Powis

6594 silver badges16 bronze badges

Sign up to request clarification or add additional context in comments.

5 Comments

Polar Bear Over a year ago

my $found = 0;

James Powis Over a year ago

fixed... in my defence it's been 5 years since I last played find the missing semicolon... Thanks!

Polar Bear Over a year ago

Please also check Modern Perl page 139 for usage of open.

perly Over a year ago

Thank you it does what i want but in your opinion is it a good idea to pass such a long string in regex pattern?

James Powis Over a year ago

@perly this does not consume the entire file all at once. It consumes the contents of the file line by line. See "Reading Files as Iterator' in devglan.com/python/file-handling-in-python for an explanation.

Collectives™ on Stack Overflow

Finding text in a file using perl program

1 Answer 1

5 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

5 Comments

Your Answer

Sign up or log in

Post as a guest

Related