Error use of uninitialized value although it is initialized - perl

Question

I am trying to make a table looking content of one input file but it constantly gives me an error
Use of uninitialized value $ac[3] in concatenation (.) or string at table.pl
line 58 (#1)
and
Use of uninitialized value $or[2] in concatenation (.) or string at table.pl
line 61 (#1)
and although I made almost every possible changes it still gives me an error and does not print well.
This is how my input file looks like:
HEADER OXIDOREDUCTASE 08-JUN-12 2LU5
EXPDTA SOLID-STATE NMR
REMARK 2 RESOLUTION. NOT APPLICABLE.
HETNAM CU COPPER (II) ION
HETNAM ZN ZINC
FORMUL 2 CU CU 2+
FORMUL 2 ZN ZN 2+
END
This is a script I am using:
#!/usr/bin/env perl
use strict;
use warnings;
use diagnostics;
#my $testfile=shift;
open(INPUT, "$ARGV[0]") or die 'Cannot make it';
my #file=<INPUT>;
close INPUT;
my #ac=();
my #dr=();
my #os=();
my #or=();
my #fo=();
for (my $line=0;$line<=$#file;$line++)
{
chomp($file[$line]);
if ($file[$line] =~ /^HEADER/)
{
print( (split '\s+', $file[$line])[-1]);
print "\t";
while ($file[$line] !~ /^END /)
{
$line++;
if ($file[$line]=~/^EXPDTA/)
{
$file[$line]=~s/^EXPDTA//;
#os=(#os,split '\s+', $file[$line]);
}
if ($file[$line] =~ /^REMARK 2 RESOLUTION./)
{
$file[$line]=~s/^REMARK 2 RESOLUTION.//;
#ac = (#ac,split'\s+',$file[$line]);
}
if ($file[$line] =~ /^HETNAM/)
{
$file[$line]=~s/^HETNAM//;
$file[$line] =~ s/\s+//;
push #dr, $file[$line];
}
if ($file[$line] =~ /^SOURCE 2 ORGANISM_SCIENTIFIC/)
{
$file[$line]=~s/^SOURCE 2 ORGANISM_SCIENTIFIC//;
#or = (#or,split'\s+',$file[$line]);
}
if ($file[$line] =~ /^FORMUL/)
{
$file[$line]=~s/^FORMUL//;
$file[$line] =~ s/\s+//;
push #fo, $file[$line];
}
}
print "$os[1] $os[2]\t";
print "\t";
#os=();
print "$ac[3] $ac[4]\t" or die "Cannot be printed"; #line 58
print "\t";
#ac=();
print "$or[2] $or[3]\t" or die "Cannot be printed"; #line 61
print "\t";
#or=();
foreach (#dr)
{
print "$_";
print "\t\t\t\t\t";
}
#dr=();
print "\n";
}
}
And this is the output it gives me, but it doesnt seems to print well and I am really not sure why:
2LU5 SOLID-STATE NMR CU COPPER (II) ION
Desired output that I am expecting is :
HEADER EXPDTA REMARK HETNAM FORMUL
OXIDOREDUCTASE 2LU5 SOLID-STATE NMR RESOLUTION. NOT APPLICABLE. COPPER (II) ION (here better to say last column because certain diversity exists before "copper") CU 2+
ZN ZINC ZN 2+

Answer 1

The root of your error is that:
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my #ac = ();
my $str = "REMARK 2 RESOLUTION. NOT APPLICABLE. ";
$str =~ s/^REMARK 2 RESOLUTION.//;
#ac = ( #ac, split '\s+', $str );
print Dumper \#ac;
The contents of #ac is:
$VAR1 = [
'',
'NOT',
'APPLICABLE.'
];
There is no $ac[3], you only have elements 0,1,2 in there.
With your #or error, you don't have any lines matching: /^SOURCE 2 ORGANISM_SCIENTIFIC/
So that array is empty, and that too, means you've got no $or[2] to print.
More generally - what you're doing here is actually really quite clunky, and there's a much cleaner solution.
How about:
#!/usr/bin/env perl
use strict;
use warnings;
#set the text "END" as our record separator
local $/ = 'END';
#define the fields to print out.
my #field_order = qw ( HEADER EXPDTA REMARK HETNAM FORMUL );
print join ( ",", #field_order), "\n"; #print header row
#iterate STDIN or file named on command line.
#just like you're doing with open (FILE, $ARGV[0])
while ( <> ) {
#select key value pairs into a hash - first word on the line is the 'key'
#and the value is 'anything else'.
my %this_entry = m/^(\w+)\s+(.*)$/gm;
next unless $this_entry{'HEADER'}; #check we have a header.
s/\s+/ /g for values %this_entry; #strip repeated spaces from fields;
s/\s+$//g for values %this_entry; #strip trailing whitespace.
#split 'header' row into separate subfields
#this is an example of how you could transform other fields.
($this_entry{'HEADER'}, $this_entry{'DATE'}, $this_entry{'STRUCT'} ) = split ' ', $this_entry{'HEADER'};
print join (",", #this_entry{#field_order} ), "\n";
}
This will - given your input - print:
HEADER,DATE,STRUCT,EXPDTA,REMARK,HETNAM,FORMUL
OXIDOREDUCTASE,08-JUN-12,2LU5,SOLID-STATE NMR,2 RESOLUTION. NOT APPLICABLE.,CU COPPER (II) ION,2 CU CU 2+
Which isn't quite what your output matches, but hopefully it's illustrated how much simpler this task could be?