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Simple examples to open a file for reading:

...

        open(my $fh, ">", "output.txt")
        or die "Can't open > output.txt: $!";

while (<$input>) {
    chomp;
    # do something with $_
}

#!/usr/bin/perl
use strict;
...
>hsa_circ_0000002|chr1:1158623-1159348-|NM_016176|SDF4
GGTGGATGTGAACACTGACCGGAAGATCAGTGCCAAGGAGATGCAGCGCTGGATCATGGAGAAGACGGCC
+GAGCACTTCCAGGAGGCCATGGAGGAGAGCAAGACACACTTCCGCGCCGTGGACCCTGACGGGGACGGT
+CACGTGTCTTGGGACGAGTATAAGGTGAAGTTTTTGGCGAGTAAAGGCCATAGCGAGAAGGAGGTTGCC
+GACGCCATCAGGCTCAACGAGGAACTCAAAGTGGATGAGGAAA
49 54

#!/usr/bin/perl
use strict;
...
>hsa_circ_0000002|chr1:1158623-1159348-|NM_016176|SDF4
GGTGGATGTGAACACTGACCGGAAGATCAGTGCCAAGGAGATGCAGCGCTGGATCATGGAGAAGACGGCC
+GAGCACTTCCAGGAGGCCATGGAGGAGAGCAAGACACACTTCCGCGCCGTGGACCCTGACGGGGACGGT
+CACGTGTCTTGGGACGAGTATAAGGTGAAGTTTTTGGCGAGTAAAGGCCATAGCGAGAAGGAGGTTGCC
+GACGCCATCAGGCTCAACGAGGAACTCAAAGTGGATGAGGAAA
49 54

#!/usr/bin/perl
use strict;
...
$ perl test.pl test.txt
Count final: 107
Count final: 107 251

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

$ cat counts.txt
107 251

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

$ cat counts.txt
107 251