I still see multiple problems. Can you show what you expect the output lines to be? I guess there is some input now on the OP. I get now:
Global symbol "$headerHash" requires explicit package name at C:\Proje
+cts_Perl\anotherfastathing.pl line 30.
Execution of C:\Projects_Perl\anotherfastathing.pl aborted due to comp
+ilation errors (#1)
    (F) You've said "use strict" or "use strict vars", which indicates
+ 
    that all variables must either be lexically scoped (using "my" or 
+"state"), 
    declared beforehand using "our", or explicitly qualified to say 
    which package the global variable is in (using "::").
    
Uncaught exception from user code:
    Global symbol "$headerHash" requires explicit package name at C:\P
+rojects_Perl\anotherfastathing.pl line 30.
    Execution of C:\Projects_Perl\anotherfastathing.pl aborted due to 
+compilation errors.

Process completed with exit code 255

[download]
Update: Ok, this looks like what you want, why not? 
#!/usr/bin/perl
use warnings;
use strict;
use diagnostics;


my $firstline = <DATA>;
my ($species) = $firstline =~ /\[(.+?)\]/;
print "$species\n";
while (<DATA>) {print;}

=Prints:
Homo sapiens
MSSDSEMAIFGEAAPFLRKSERERIEAQNKPFDAKTSVFVVDPKESFVKATVQSREGGKVTAKTEAGATV
+TVKDDQVFPM
NPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQE
+APPHIFSISD
NAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGEKKKEEVTSGKMQGTLEDQIISANPLL
+EAFGNAKTVR
NDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNP
+YDYAFVSQGE
ITVPSIDDQEELMATDSAIEILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYL
+QNLNSADLLK
ALCYPRVKVGNEYVTKGQTVQQVYNAVGALAKAVYDKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEI
+FDFNSLEQLC
INFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTS
+FKNKLYEQHL
GKSNNFQKPKPAKGKPEAHFSLIHYAGTVDYNIAGWLDKNKDPLNETVVGLYQKSAMKTLALLFVGATGA
+EAEAGGGKKG
GKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICR
+KGFPSRILYA
=cut


__DATA__
>gi|115527082|ref|NP_005954.3| myosin-1 [Homo sapiens] >gi|226694176|s
+p|P12882.3|MYH1_HUMAN RecName: Full=Myosin-1; AltName: Full=Myosin he
+avy chain 1; AltName: Full=Myosin heavy chain 2x; Short=MyHC-2x; AltN
+ame: Full=Myosin heavy chain IIx/d; Short=MyHC-IIx/d; AltName: Full=M
+yosin heavy chain, skeletal muscle, adult 1 [Homo sapiens] >gi|119610
+411|gb|EAW90005.1| hCG1986604, isoform CRA_b
MSSDSEMAIFGEAAPFLRKSERERIEAQNKPFDAKTSVFVVDPKESFVKATVQSREGGKVTAKTEAGATV
+TVKDDQVFPM
NPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQE
+APPHIFSISD
NAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGEKKKEEVTSGKMQGTLEDQIISANPLL
+EAFGNAKTVR
NDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNP
+YDYAFVSQGE
ITVPSIDDQEELMATDSAIEILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYL
+QNLNSADLLK
ALCYPRVKVGNEYVTKGQTVQQVYNAVGALAKAVYDKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEI
+FDFNSLEQLC
INFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTS
+FKNKLYEQHL
GKSNNFQKPKPAKGKPEAHFSLIHYAGTVDYNIAGWLDKNKDPLNETVVGLYQKSAMKTLALLFVGATGA
+EAEAGGGKKG
GKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICR
+KGFPSRILYA

[download]

In reply to Re^3: While loop with nested if statements by Marshall
in thread While loop with nested if statements by lairel

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