A different approach might be to use the $/ variable ( see perlvar for details ) to read in each record and then test whether it has the 'pairs' field:

use warnings;
use strict;

{
        ## modify input record separator to read
        ## each FASTA record separately
    local $/ = '>';
        
        ## test each record, printing out if it has
        ## pair field
    while (<DATA>){
        print $_ if ($_ =~ /pair:\d+/);
    }
}
__DATA__
>CVSF43567.d1 bg|346280
CGTAGCTGATGCTGTGCTGTTGTGTCGGGGGGATATATATATATATATGGGGTCGTAGTCGTAGCGCTAG
TATGCTAGCAGCGTAGATGCTGATCGATGCTGATGCTGATCGTAGTCGTAGGCTAGTGCGATCGTAGTCG
TAGTCGATGCTGATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAG
TGCTCGATGCTAGTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGCTAGCACGTAGCTG
GCTCGATGCTGATGCTGAT
>CVSF10000.x1 bg|356789 pair:789860
ATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAGTGCTCGATGCTA
GTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGATGCTGACTGATGCTGATCTGTACGT
CGTAGCTGATGCATGCGCTAGTAGCT
>CVSF10000.y1 bg|356790 pair:789859
GCTAGTCGATGCTGATGCTGTAGCTAGCGTAGTCGTACGCGCGCGCGCGCGTTTTTTGTGACGTCGTAGT
CCGTAGCTGATGCGATGCTAGTGCTGTGTCAGCTGATGTCGTGTGTAGCTGATGCTGATCGTTCGTGTGT
CGATGCTGATGCTAGTCGTAGTGTAT

[download]

In this case I am simply testing for the presence of the 'pair' field using a regex (see perlre). Hope this helps!

Just a something something...

In reply to Re: Print the data following few specific lines in perl by BioLion
in thread Print the data following few specific lines in perl by ad23

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