Hello everybody,

I'm searching a file of annotations for a select list of terms in a second file. It seems to work fine but I'd like to learn alternative ways to do it or learn how to improve it. Specifically, is there is a way I can improve the regular expressions in this line:

 /(\b($term)\b|$term-)\b|(-$term)\b/i) {

Thanks!

Here is the full script:

#!/usr/bin/perl
# Read search terms into array @terms
open (SRC, $searchTermsFile) || die "can't open search terms file";
@terms = <SRC>;
chomp (@terms);
@terms = sort @terms;
my @annotationlist;
#-------------------------------------------------------
# Search each line in annotations file for match with search terms
%nTermHits = ();
$nTotalHits = 0;
open (ANN, $annotationsFile) || die "$annotationsFile won't open\n";
while ($line = <ANN>) {
    #chomp($line);
    @fields = split(/\t/, $line);
    $annotation = $fields [2];
    foreach $term (@terms) {
        if($annotation =~ /(\b($term)\b|$term-)\b|(-$term)\b/i) {
            $nTermHits {$term}++;
            $nTotalHits++;
            push(@annotationlist, "$annotation\n");
    }
}}
#@annotationlist = sort @annotationlist;
#print "@annotationlist\n";
#---------------------------------------
foreach $term (@terms) {
    if ($nTermHits {$term} > 0) {
        printf "%s\t%d\n", $term, $nTermHits {$term};
    }
}
print "Total hits: $nTotalHits\n";
#-----------------------------

[download]

This is the output :

Ras GTPase    3
catalase    2
cysteine proteinase    4
Total hits: 9

[download]

In reply to Help to improve script that searches a file for key words in a second file. by mastarr

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