Perhaps something along the lines of

#!/usr/bin/perl

use warnings;
use strict;

my (@peptide, @cds);
while (my $line = <DATA>){
  next unless $line =~ /^>/;
  chomp $line;
  chomp(my $seq = <DATA>);
  if ($line =~ /peptide/){
    push @peptide, $line, $seq;
    # or print to file handle
  }
  elsif ($line =~ /CDS/){
    push @cds, $line, $seq;
    # or print to file handle
  }
}

print qq{$_\n} for @peptide;
print qq{---\n};
print qq{$_\n} for @cds;

__DATA__
GENSCAN 1.0 Date run: 11-Mar-109  Time: 00:29:37

Sequence scaffold_2 : 47583 bp : 37.42% C+G : Isochore 1 ( 0 - 100 C+G
+%)

Parameter matrix: test.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.01 Init -   2604   2462  143  0  2   77   96   184 0.883  20.81
 1.00 Prom -   3677   3638   40                               2.82

 2.00 Prom +   4382   4421   40                               1.62
 2.01 Init +   6395   6399    5  1  2   73   84     0 0.122  -0.16
 2.02 Intr +   8270   8412  143  2  2   74   82   110 0.141  12.00
 2.03 Term +   8516   8523    8  0  2   46   46     0 0.473  -8.05
 2.04 PlyA +   9723   9728    6                               2.27

Predicted peptide sequence(s):

Predicted coding sequence(s):


>scaffold_2|GENSCAN_predicted_peptide_1|48_aa
MDRSHQIWDEKLMDQKCVLYPVCLWHEQESEMNWEAEKAERLRTEQKX

>scaffold_2|GENSCAN_predicted_CDS_1|144_bp
atggatcggagtcatcagatatgggatgagaagctgatggatcagaagtgcgtcctctac
cccgtctgcctctggcacgagcaggagagcgagatgaactgggaggctgagaaagctgag
aggctaaggactgaacagaaaggn

>scaffold_2|GENSCAN_predicted_peptide_2|51_aa
MRKNEGVDDADPLIEGMKEITLKDSATPEDKDQEDKQDERGEEIQEQPQEM

>scaffold_2|GENSCAN_predicted_CDS_2|156_bp
atgaggaagaatgagggtgttgatgatgcagatccactaatagaaggtatgaaggagatc
actctgaaagattcagcaactccagaagacaaggatcaagaagacaaacaagatgagaga
ggtgaagaaattcaagaacaacctcaagagatgtag
[download]

>scaffold_2|GENSCAN_predicted_peptide_1|48_aa
MDRSHQIWDEKLMDQKCVLYPVCLWHEQESEMNWEAEKAERLRTEQKX
>scaffold_2|GENSCAN_predicted_peptide_2|51_aa
MRKNEGVDDADPLIEGMKEITLKDSATPEDKDQEDKQDERGEEIQEQPQEM
---
>scaffold_2|GENSCAN_predicted_CDS_1|144_bp
atggatcggagtcatcagatatgggatgagaagctgatggatcagaagtgcgtcctctac
>scaffold_2|GENSCAN_predicted_CDS_2|156_bp
atgaggaagaatgagggtgttgatgatgcagatccactaatagaaggtatgaaggagatc
[download]