Yes, I tried that but it wasn't very successful (seeing as my grasp of hashes is rather pathetic)

Here is what you need to do:
1. Declare a hash
2. Read the first file line by line, populating the hash
3. iterate over the second file, and look up the values in the hash

In your current program, you compare things to $pdbchain, so your hash keys have to be constructed exactly in the same way as $pdbchain

Give it a try, and when you have problems, come back with more specific questions.

Please, when you have an instance like this, post your code. Doubtless someone here can find and correct the error. If you can't post it because it's long since been over-written, I'd suggest you look into a Version Control System. Sometimes good approaches get discarded because a detail or two gets in the way.

HTH,

planetscape

I'm sure there will be a fair number of people giving specific code advice. I'll give programming advice:

Once you know you have speed problems, profile. Don't assume you know what is fast and what is slow, and don't assume you know what is being run the most often.

There is an adequate profiler that comes with Perl, that being Devel::DProf. Read up, and see what the basics are. It will help in many cases, but isn't all that extensive.

A better profiler is available in Devel::NYTProf, which will tell you exactly how many times each line of code (or block, or subroutine) is called, and how long it took. Feed your program to that with a representative sample of your data, and work out ways to avoid the slowest operations.

Good general advice, but but profiling the OPs code won't tell you anything that isn't readily apparent from a cursory inspection.

Matching N elements from one file against M elements from a second, by iterating through an array containing the M elements--and respliting each element each time through--it is obvious enough where the problems lie.

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

"Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."

Thats really good advice. Thanks. Definitely something to remember

I'm not exactly a super expert or anything, but this script might get you where you want to go. Beware, I've only done minimal testing, and just on the data you provided. It also comes with the caveat (as has been previously mentioned) that it'll very much depend on the size of these files. However since you are reading them into memory in your initial script, its probably going to be alright.

#!/usr/local/bin/perl

use strict;
use warnings;

my $resfile = shift;
my $csafile = shift;

open(RESFILE, "$resfile") or die "unable to open $resfile: $!\n";
open(CSAFILE, "$csafile") or die "unable to open $csafile: $!\n";
open(OUTFILE, ">outfile") or die "Can't open the outfile: $!\n";

my %REShash;
#concatenate number and id for (hopefully) unique hash key
while (<RESFILE>){
    /([A-Z])\s(\d+)\s([0-9a-zA-Z]+)/;
    my $currentID = $3.$2;
    $REShash{$currentID}=$1;
}

while(<CSAFILE>)
{
    chomp;
   my @record = split (/,/, $_);
   #concatenate all parts of the record to get same formated hash key
   my $currentId= $record[0].$record[3].$record[4];
   if (exists $REShash{$currentId}){
   print OUTFILE join(',', @record)."\n";
   }
}
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Also, what is being printed to the "outfile" is in the form of what I believe you are calling the CSAFILE (I may have those two switched around), fyi

It looks like you want something like:

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

my $resfile = shift;
my $csafile = shift;

open my $RESFILE, '<', $resfile or die "unable to open $resfile: $!\n"
+;

my %hashlookup;
while ( <$RESFILE> ) {
    my ( undef, $num, $str ) = split;
    $hashlookup{ substr( $str, 0, 5 ) . " $num" } = 1;
    }
close $RESFILE;

open my $CSAFILE, '<', $csafile or die "unable to open $csafile: $!\n"
+;

while ( <$CSAFILE> ) {
    chomp;
    my ( $pdb, $chain, $csanum ) = ( split /,/ )[ 0, 3, 4 ];
    my $key = "$pdb$chain $csanum";
    print "$key\n" if $hashlookup{ $key };
    }
close $CSAFILE;
[download]