Help with program for proteins

[jemswira]

So I recently posted up this code on perlmonks asking for help, and got it to work properly(THANKS)

$/="\/\/";
our @acnumbers=qw(P0A252 Q9AT80 Q0HKB6);
our $acnumbers;


foreach $acnumbers(@acnumbers){
    my $unit;
    foreach $unit(<PFAMDB>){
        my @units= split /#/,$unit;
        my @pfx=grep(/=GF AC/,@units);
        our $units;
        foreach $units(@units){
            if ($units=~/.*AC $acnumbers/){
            push (@list, @pfx);
            }else{next}
        }
    
    }
    print "$acnumbers is in:";
    print @list;
    undef @list;
}

So what it did was to take this data

# STOCKHOLM 1.0

#=GF ID 1-cysPrx_C

#=GF AC PF10417.4

#=GF DE C-terminal domain of 1-Cys peroxiredoxin

...

#=GS D8BPP0_ECOLX/154-186 AC D8BPP0.1

#=GS D6I5T0_ECOLX/154-186 AC D6I5T0.1

...

//

...

find the PFxxxx number and whether the AC xxxxxx number was in it.

There's another file, which has many lines of:

>tr|A0A171|A0A171_PYRHR Glutamate synthase small subunit-like protein 1 OS=Pyrococcus horikoshii GN=gltY PE=4 SV=1

and i need to get the A0A171, and A0A171_PYRHR Glutamate synthase small subunit-like protein 1 out also, then run the first code. So i got this:

foreach (<DATABASE>){push (@uniprot,$_);}

my $i;
my $name;
    foreach $uniprot(@uniprot){
    our $acc;
    my @splitted=split /\||=/,$uniprot;
    
    foreach $i(@splitted){
        if ($i=~/\b\w{6}\b/ and $i !~/\_/){
            $acc=$i;
        }
        elsif ($i=~ /.+(?= OS)/){
            $name=$i;
        }
        else {next;}
    
    my $unit;
$/="\/\/";
open PFAMDB, 'C:\Users\Jems\Desktop\Perl\PFAM.txt' or die $!;    
    foreach $unit(<PFAMDB>){
        my @units= split /#/,$unit;
        my @pfx=grep(/=GF AC/,@units);
        
        our $units;
        foreach $units(@units){
        

            if ($units=~/.*AC $acc/){
            push (@list, @pfx);
            
            }else{next}
        }
    
    }
    print "$acc, also called $name, is in:"
    print @list;
    
    undef @list;
}}

however it no longer seems to get @list out. @pfx is still correct when i print tested, but it no longer pushes to @list. (I THINK)

so is it that i am doing anything wrong? also, how would i remove the OS at the back of $name, and the #=GF AC and everything after the fullstop in @pfx? Thanks in advance!

[RichardK]

Are you using strict and warnings?

Where does $acc come from in

if ($units =~ /.*AC $acc/)

[jemswira]

foreach $i(@splitted){
        if ($i=~/\b\w{6}\b/ and $i !~/\_/){
            $acc=$i;

If the accession number in the first file matched one in a line of the second one, then I'd push @pfx into @list. at least that was the plan

[umasuresh]

I always use ptkdb to debug the problem:
Re: Parse variables