Hi PerlMonks,

There are four samples (sample1...sample4) each with a different name. Sample 1 & 2 have the same sequence i.e. ATGC. Likewise, sample 3 & 4 have same sequence i.e. CCGG. My interest is to retain only the sample 1 with sequence ATGC and reject sample 2 as the latter shares the same sequence with sample 1. Same is the case for sample 3 & sample 4 i.e. I wish to retain sample 3 and reject sample 4. I am at my wit's end to fix this problem. I am looking forward to suggestions from perl monks regarding this problem.

I have written a script t2.pl (given below) to separate the header and the sequence. Here goes the script:

#!/usr/bin/perl 
use warnings; 
use strict;  

my $a=">sample1 ..sequence
ATGC fun
>sample2 ..sequence
ATGC fun
>sample3 ..sequence
CCGG fun
>sample4 ..sequence
CCGG fun"; 

 while ($a=~ />.*?fun/gs) {my $trial1=$&; my $trial2=$&;     

    while ($trial1=~ />.*sequence/gs) {my $header=$&;  
           $trial2=~ s/($header)//gs; 
           my $seq=$trial2; 
           $seq=~ s/\s//;
           $seq=~ s/fun//;   

    print "\n Header: $header
 Sequence: $seq\n"; 
    } 
 } 
# code?? 
exit;
[download]

I have got the results like:

 C:\Users\x\Desktop>t2.pl

 Header: >sample1 ..sequence
 Sequence: ATGC

 Header: >sample2 ..sequence
 Sequence: ATGC

 Header: >sample3 ..sequence
 Sequence: CCGG

 Header: >sample4 ..sequence
 Sequence: CCGG
[download]

But the expected results should look like:

>sample1 ..sequence
ATGC
>sample3 ..sequence
CCGG
[download]