hi monks, i have 2 files, i need to extract some data from one file based on another file. the data file is around 1GB. Since, its too big to read line by line, i got this idea to read it at their positions. I used tell and seek functions. But i have problems in getting the desired output. check out my code. 
file1:
SID834.56    AGAAGTCGTACGATCA
SID164.26    AGTCGATCATTATATATTCGCTAG
SID4.56    AGCTAGCGATCGATCCCCCCCCCCCCCCCC
SID5764.12    CGATCGATC
SID564.12    ACGAATATGATAC

file2:
cluster number 1: (reads count:2)
    SID834.56
    SID564.12
cluster number 2: (reads count:2)
    SID164.26
    SID5764.12
cluster number 3: (reads count:1)
    SID4.56

code:
#!/usr/bin/perl -w
use strict;
use warnings;

open(FH1,$ARGV[0]) or die "can not open\n";
open(FH2,$ARGV[1]) or die "can not open\n";

my @indx;

while(<FH1>){
    my ($id,$seq)=split("\t",$_);
    push(@indx, "$id\t".tell FH1);
}


while(<FH2>){
    if($_=~m/^clus/){
        my $clushead=$_;
        print "\n$clushead";
    }
    else{
        $_=~s/\t//g;$_=~s/\n//g;
        my $tes=$_;
        my @hit=grep(/$tes/,@indx);        
        my $sca="@hit";
        my ($id1,$pos)=split("\t",$sca);
        print sysseek (FH1,$pos,0),"\n" or die "seek:$!";
    }
}

desired results:
cluster number 1: (reads count:2)
SID834.56    AGAAGTCGTACGATCA
SID564.12    ACGAATATGATAC
cluster number 2: (reads count:2)
SID164.26    AGTCGATCATTATATATTCGCTAG
SID5764.12    CGATCGATC
cluster number 3: (reads count:1)
SID4.56    AGCTAGCGATCGATCCCCCCCCCCCCCCCC

results which i get now:
cluster number 1: (reads count:2)
27
146

cluster number 2: (reads count:2)
62
122

cluster number 3: (reads count:1)
101

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why is the seek function not fetching the content but the position? thanks !!!

In reply to seeking help for seek function by pearly

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