Using the supplied data and code (modified so the data is inlined in the code):

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

my $data2 = <<D2;
A5V
A5S
...
I152T
D2

my $data1 = <<D1;
>gi|134611|sp|P00441.2|_Homo_sapiens ...
END
D1

my $data1Name = \$data1;
open my $inFile, '<', $data1Name or die "Failed at opening $data1Name:
+ $!\n";

...
[download]

I get 78 lines of output starting:

This is [GI: 134611] and [Accession: P00441]
VARIANT        POTENTIAL        PD
A5V    A{229365862} -{110180503} -{134284932} -{226232347} A{185132317
+} -{62550923} A{134611} -{12733941} A{62858937} A{226372562} A{225706
+520} A{112419222} A{238801237} A{47227092} -{216963348} A{56790262} A
+{116048074} -{54873355} A{185135289} -{151549024} A{27462182} -{22693
+4254}    
A5S    A{229365862} -{110180503} -{134284932} -{226232347} A{185132317
+} -{62550923} A{134611} -{12733941} A{62858937} A{226372562} A{225706
+520} A{112419222} A{238801237} A{47227092} -{216963348} A{56790262} A
+{116048074} -{54873355} A{185135289} -{151549024} A{27462182} -{22693
+4254}
[download]

and ending:

I150T    I{229365862} -{110180503} -{134284932} -{226232347} I{1851323
+17} -{62550923} I{134611} -{12733941} I{62858937} I{226372562} I{2257
+06520} I{112419222} I{238801237} I{47227092} I{216963348} I{56790262}
+ I{116048074} -{54873355} I{185135289} I{151549024} I{27462182} -{226
+934254}    
I152T    I{229365862} -{110180503} -{134284932} -{226232347} I{1851323
+17} -{62550923} I{134611} -{12733941} L{62858937} I{226372562} I{2257
+06520} F{112419222} I{238801237} I{47227092} I{216963348} I{56790262}
+ I{116048074} -{54873355} I{185135289} -{151549024} I{27462182} -{226
+934254}
[download]

In what fashion is that not what you expected?