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Your homepage says you're new to programming, so I thought I'd add some missing bits of code (in bold) in case you were not aware that they should be there.
NB I have not changed/fixed the logic of your code.
#!usr/bin/perl -w
use strict;
use warnings;

open(IN,"/home/maize/sequence-ID.txt") || die $!;
open(OUT,">abc.txt") || die $!;
open(OUT1,">blastresults.txt") || die $!;

while(my $id=<IN>)
    open(BLAST,"output/$id") || die $!;
    while(my $file=<BLAST>)
        if ($file=~ m/No hits found/)
            print OUT "$id \n";
    close(BLAST) || die $!;
close(IN) || die $!;
close(OUT) || die $!;
close(OUT1) || die $!; 
If you prefer you can use normal Perl variables instead of file handles

    open(my $blast,"output/$id") || die $!;
    while(my $file=<$blast>)
        if ($file=~ m/No hits found/)
            print OUT "$id \n";
    close($blast) || die $!;


If you're looking for some good books, I can highly recommend these 3 books which form a 3 part series:
Learning Perl: Making Easy Things Easy and Hard Things Possible
Intermediate Perl: Beyond The Basics of Learning Perl
Mastering Perl: Creating Professional Programs with Perl

I just happened to notice this. I have no idea what it it like, but it might be just what you want:
Mastering Perl for Bioinformatics

In reply to Re: how do i obtain blast result from the given file by zork42
in thread how do i obtain blast result from the given file by bingalee

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