Hello lairel,

When I run your code with perl -c, I get the following output:

What this is telling you is that the variable $headerHash is being used where it hasn’t been declared. That’s because a variable declaration with my (which produces what is called a lexical variable) has a scope which is limited to the block where it occurs (see e.g. the tutorials in Variables and Scoping). So in this code:

while (<INFILE>){
    chomp;
    my $line = $_;
    ...
    if ($line =~ /^>/){
        my $header = $line;
        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
            my $headerHash;                                 # A
            $headerHash{$1} = $2;
        }
        else{
            my $seq = $line;
            print OUTFILE $headerHash, "\n", $seq, "\n";    # B
        }
    }
}
[download]

the declaration at point A has gone out of scope by the time the variable is referenced at point B. To fix this, you need to give the variable a wider scope, by declaring it before you enter the if/else construct:

while (<INFILE>){
    chomp;
    my $line = $_;
    my $headerHash;
    ...
    if ($line =~ /^>/){
        my $header = $line;
        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
            $headerHash{$1} = $2;
        }
        else{
            my $seq = $line;
            print OUTFILE $headerHash, "\n", $seq, "\n";
        }
    }
}
[download]

But while this will remove the compile error, it doesn’t make a lot of sense: you print out the value of $headerHash only if its value has not been initialised! Perhaps you need to declare $headerHash before the while loop? In any case, a line such as:

print OUTFILE $headerHash ...
[download]

will only result in output like this:

16:17 >perl -wE "my $h = { a => 1, e => 2 }; print STDOUT $h;"
HASH(0x3ac320)
16:30 >
[download]

which is not what you want. Please supply a sample input file, together with the output you want to produce from that file (see How do I post a question effectively?). This will help the monks to understand what you’re really trying to achieve.

Update:

Until I read Marshall’s reply, I hadn’t noticed that %headerHash is already declared before the loop; I was reading the line $headerHash{$1} = $2; as though it were this: $headerHash->{$1} = $2; — i.e., treating $headerHash as a hash reference — which of course it isn’t. :-(

lairel, just to emphasise the point Marshall is making: in Perl, $headerHash, @headerHash, and %headerHash are separate, completely unrelated variables. $headerHash{$key} references one element of the hash %headerHash, and is unrelated to the scalar variable $headerHash.

Hope that helps,

G'day lairel,

"I keep getting errors about uninitialized variables and needing explicit declaration."

Those error messages should tell you the variable involved and other information: use this to track down your problem. If you need help with any particular error message(s), you'll need to show us the text also.

"I have tried so many things that I am lost and confused ..."

You need to understand fundamental constructs, such as while loops. I suggest you read "perlintro -- a brief introduction and overview of Perl".

Consider this technique for accessing fasta files for this type of work:

#!/usr/bin/env perl

use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        $_ = substr $_, 1 if $. == 1;

        my ($head, $data) = split /\n/;

        if ($head eq $ARGV[0]) {
            print "Found! Head: '$head'; Data: '$data'\n";
            last;
        }
    }
}

__DATA__
>head1
data1
>head2
data2
>head3
data3
[download]

Some test runs:

$ pm_1159403_fasta.pl head1
Found! Head: 'head1'; Data: 'data1'
$ pm_1159403_fasta.pl head2
Found! Head: 'head2'; Data: 'data2'
$ pm_1159403_fasta.pl head3
Found! Head: 'head3'; Data: 'data3'
[download]

See also: $/ - input record separator; $. - input line number.

However, some things look odd to me:

my $headerHash;
$headerHash{$1} = $2;
[download]

Update: Even if you move my $headerhash; above the while loop, On line 28, print OUTFILE $headerHash, "\n", $seq, "\n";, that will create a runtime error because there is nowhere that I can see where this scalar $headerhash is assigned any value, it will be "undef".

Maybe you are confused about hash syntax? A hash like %headerhash is accessed with 2 things, a key and a value, like $hash{$key}=$value.

Be careful, something like %hash=55; doesn't do what you think!! This increases the size of the hash, i.e. more buckets. This doesn't assign a value to the hash. Consider:

#!/usr/bin/perl
use strict;

my %hash;             #defaults to 8 buckets
$hash{a}=33;          #use one of the buckets
my $buckets = %hash;

print "$buckets\n"; #prints 1/8, 1 of 8 buckets used
keys(%hash)=32;     #increase size of hash to 32 buckets
$buckets = %hash;
print "$buckets\n"; #prints 1/32 1 of 32 buckets used
[download]

I've added an example of the input and output to my original post, and my code is currently looking like this, but again I am still not sure I am using the hash correctly, and the hash key is really throwing me. I'm not getting any errors with this code, but my output file is empty

#!/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 =~ /^>/){
                 $header = $line;
                        if ($header =~ /(>gi.*)\[(.+)\](>g.*)\[(.+)\]/
+){
                                my $headerHash = $2;
                                $headerHash{$2} = $2;
}
                        }
                else {
                 $seq = $line;

        }
}
close INFILE;
for my $key(keys %headerHash){

print OUTFILE $headerHash{$key}, "\n", $seq, "\n";
}
[download]

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]