Hi guys. So I have tried to make a database combining two files of data. One is accesionnumbersfull.txt

A0AQI4
A0AQI5
A0AQI7
.....

[download]

the other is this Pfam-A.seed

# STOCKHOLM 1.0
#=GF ID   1-cysPrx_C
#=GF AC   PF10417.4
#=GF DE   C-terminal domain of 1-Cys peroxiredoxin
#=GF AU   Finn RD, Coggill PC
#=GF SE   Gene3D, pdb_1prx
...
#=GS A3EU39_9BACT/160-195  AC A3EU39.1
#=GS Q7VQB3_BLOFL/159-194  AC Q7VQB3.1
#=GS Q057V5_BUCCC/160-195  AC Q057V5.1
#=GS A5CDZ8_ORITB/160-195  AC A5CDZ8.1
...

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So what i'm supposed to do is to match the numbers in the first file to the groups in the second. so the group name is after the #=GF AC. PFxxxxx Problem is the files are huge. the first file alone is 138mb. So i have memory issues. my code is as follow.

#!/usr/bin/perl
use warnings;
use strict;
open OUTPUT, ">C:\\Users\\Jems\\Desktop\\Perl\\PFAMin.txt" or die $!;
open ANUMBER, "C:\\Users\\Jems\\Desktop\\Perl\\AccessionNumbersfull.tx
+t" or die $!;
our @acnumbers;
select OUTPUT;
$|=1;
foreach (<ANUMBER>){
    chomp;
    push (@acnumbers, $_);}
$/="\/\/";

our $acnumbers;
our @list;

foreach $acnumbers(@acnumbers){
    
    open PFAMDB, "C:\\Users\\Jems\\Desktop\\Perl\\Pfam-A.seed" or die 
+$!;
    my $unit;
    foreach $unit(<PFAMDB>){
        my @units= split /#/,$unit;
        my @pfx=grep(/=GF AC/,@units);
        foreach (@pfx){s/=GF AC/\x20/};
        our $units;
        foreach $units(@units){
            if ($units=~/.*AC $acnumbers/){
            push (@list, @pfx);
            }else{next}
        }
    
    }
    
    print "$acnumbers is in:";
    print "@list \n";
    undef @list;
}

[download]

anyway to streamline it?

another thing i needed to do is add the names corresponding to the numbers. those are in a seperate file, but the sequence is the same. i took the numbers out of that file. format:

>tr|A0FGZ9|A0FGZ9_9ARCH Methyl coenzyme M reductase (Fragment) OS=uncu
+ltured archaeon GN=mcrA PE=4 SV=1
>tr|A0FH03|A0FH03_9ARCH Methyl coenzyme M reductase (Fragment) OS=uncu
+ltured archaeon GN=mcrA PE=4 SV=1

[download]

but i don't know how to. any ideas? thanks!!

sorry but it's kinda urgent and i've been trying for ages!

In reply to Using less memory with BIG files by jemswira

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