I keep getting errors about uninitialized variables and needing explicit declaration. I have tried so many things that I am lost and confused and can't remember what I have tried :( The goal of this program is to read in a file, and search the header for the name, then return only the name of the header and the non-header line. I have some of the attempts commented out, but this is what I currently have

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

open( INFILE, "<", 'myosin.fasta') or die $!; #open original myosin.fa
+sta for reading
open( OUTFILE, ">", 'modifiedHeaders.fasta') or die $!; #open/create n
+ew fasta for writing

my %headerHash; #create hash for the header
my %seq;
my %header;

#loop through old file 
while (<INFILE>){
        chomp;
        my $line = $_;
# use if/then to seperate headers from seq, while regex to select only
+ species name in header
                if ($line =~ /^>/){
                my $header = $line;
                        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]
+/){
my $headerHash;
$headerHash{$1} = $2;
                #       return $headerHash;
                        }
                else{
                my $seq = $line;
        #       return $seq ;
print OUTFILE $headerHash, "\n", $seq, "\n";
                }
#       if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
#       my $headerHash = $2;}   

#print $headerHash
#       print OUTFILE $headerHash{$2}, "\n", $seq, "\n";
                }
}
#print OUTFILE $headerHash, "\n", $seq, "\n";

[download]

here is an example of the input

>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]

the desired output for that should be: 

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

[download]

In reply to While loop with nested if statements by lairel

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