#!/usr/bin/env perl -l

use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        $_ = substr $_, 1 if $. == 1;
        chomp;
        my ($key, @seq_parts) = split /\n/;
        print "KEY=|$key|";
        my $seq = join '', @seq_parts;
        print "SEQ=|$seq|";
    }
} 

__DATA__
>ENSCAPT00000000001.1 cdna (...)
CACTCCGCCGGCAAGGCCACCAAGTATCTGAAGGATGTCACGTTAAAGAAGCAATGTGTG
CCATTCCGGCGTTACAATGGTGGAGTTGGAAGGTGTGCCCAGGCCAAACAATGGGGCTGG
ACCCAGGGTCGGTGGCCCAAAAAGAGTGCTGAATTTTTGCTGCAC
>ENSCAPT00000000002.1 cdna (...)
CAGCTGCTGAAGACGGAGCTGGGGTCCTTCTTCACCGAGTACCTGCAGAACCAGCTGCTG
ACCAAAGGCATGGTGATCCTTCGGGACAAGATCCGCTTCTATGAGGGACAGAAACTGCTG
GACTCGCTGGCAGAGACCTGGGACTTCTTCTTCAGCGACGTGCTGCCCACGCTGCAGGCC
ATCTTCTACCC
>ENSCAPT00000000004.1 cdna (...)
ATGATGCTGGGAGAAGATGATGAGGAGTTCGTGGTGAAGGTGCGGGGTTTGCCTTGGTCC
TGCTCGGCTGACGAGGTGCAGCGGTTCTTCTCCGACTGCAAAATTCAAAATGGTGCTCAA
GGTATTTGTTTCATCTACACCAGAGAAGGCAGACCGAGTGGCGAGGCTTTTGTTGAACTT
GAATCCGAAGATGAAGTCAAACTATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCAT
ACTGGTCCAAATAGTCCTGACACGGCCAATGATGGCTTTGTACGGCTTAGAGAACTCCCC
TTTGGATGTAGCA