Maybe this is what you are looking for.

use warnings;
use strict; 

open( F1, "subsettest.txt" ) or die "file1: $!";
open( F2, "subsettest1.txt" ) or die "file2: $!";

while ( my $s1 = <F1> ) {
   my $s2 = <F2>;
   if ( $s1 =~ /^>/ ) {
      print $s1;
   } else {
      print $s2,$s1;  
   }
}
close F1;
close F2;
exit;

[download]
>GK9PVB108JH8SN rank=0000021 x=3781.0 y=885.0 length=137
40 38 38 30 30 30 38 40 40 30 30 30 36 40 40 40 40 40 40 40 40 40 40 4
+0 39 34 34 14 14 14 14 13 19 14 18 25 32 32 34 27 
TGATTATGAGTTAGATGTTCGCTCTGAGGTTTCAACGATGCTTCAAGATTCCTAATTCGCGTTGCGACTC
+TCGAGTATGCGTTCTATTCACATTTCTGTTGTCGTACATATTTGACTCACGATCTTGATTTCTTATC
>GK9PVB108JYDQ5 rank=0000032 x=3965.0 y=143.0 length=53
25 21 21 23 23 37 31 31 31 37 37 39 38 40 40 40 40 40 40 40 40 39 39 3
+9 39 35 23 25 25 37 34 35 36 37 37 37 37 37 39 39 40 40 40 40 39 38 3
+5 33 33 33 32 31 19 
GTTTTCAACGCTGGTTCGAGATTTCCTAATTTCACATTGCGACTCTCGAGTGC

[download]

In reply to Re^2: combine 2 fasta files into 1 by Generoso
in thread combine 2 fasta files into 1 by newbie25

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