Hello Monks,

I'm trying to master the art of searching with hashes. I have a file with a list of search terms (one line = one term):

J00153:42:HC5NCBBXX:6:1101:10896:14959
J00153:42:HC5NCBBXX:6:1101:10896:14959
J00153:42:HC5NCBBXX:6:1101:26616:20709
J00153:42:HC5NCBBXX:6:1101:27549:19935

[download]

...and a master file I want to search for those terms in (again, one line per record):

 J00153:42:HC5NCBBXX:6:1101:10896:14959    99    gnl|Btau_4.6.1|chr16 
+   72729218    1    12M
J00153:42:HC5NCBBXX:6:1101:27549:19935    83    gnl|Btau_4.6.1|chr8   
+ 49556412    1    7M

[download]

I started by opening the query file and reading each line into an array. Then while-ing through the master file, returning matching lines where the array elements match the relevant part of the master file:

# Open query file and read into array
$queryfile = $ARGV[0];
open (QUERYFILE, $queryfile) or die "Cannot open query file\n";
@queries = <QUERYFILE>;
close QUERYFILE;

# Open main file
$mainfile = $ARGV[1];
open (MAINFILE, $mainfile) or die "Cannot open searchable file\n";

# Search through main file
while ($inline = <MAINFILE>) {
    @split = split /\t/, $inline;
    $ID = $split[0];
    
    if (grep /$ID/, @queries) {
        print $inline;
        }
        else {
        }
    
    }
    
exit;

[download]

This works fine, but the files are huge and the code takes an age to run. So, I tried converting the array to a hash (array elements = hash keys, values all = 1) but I can't seem to get the pattern matching syntax right; the code runs much faster but nothing comes back. So far I have:

# Open query file and read into array
$queryfile = $ARGV[0];
open (QUERYFILE, $queryfile) or die "Cannot open query file\n";
@queries = <QUERYFILE>;
close QUERYFILE;

# Convert array to hash
%hash = map {$_ => 1} @queries;

# Open main file
$mainfile = $ARGV[1];
open (MAINFILE, $mainfile) or die "Cannot open searchable file\n";

# Search through main file
while ($inline = <MAINFILE>) {
    @split = split /\t/, $inline;
    $ID = $split[0];
    
    if (defined $hash{$ID}) {
        print $inline;
        }
        else {
        }
    }
exit;

[download]

Any Perly wisodom greatly appreciated!

In reply to Hash searching by Oligo

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