CODEWITHSUNDEEP
arraysperl
user3781528
user3781528

Reputation: 639

Perl find similar elements from two arrays

I would like to retrieve elements from @amplicon_exon array that contain similar element (like) to @failedamplicons array. Each element in @failedamplicons is unique and can only match a single element from @amplicon_exon. I've tried two for loops but get repeat values. Is there a better way of finding and retrieving similar values from the two arrays?

@failedamplicons: example:
OCP1_FGFR3_8.87
OCP1_AR_14.89

@amplicon_exon: example:
TEST_Focus_ERBB2_2:22:ERBB2:GENE_ID=ERBB2;PURPOSE=CNV,Hotspot;CNV_ID=ERBB2;CNV_HS=1
OCP1_FGFR3_8:intron:FGFR3:GENE_ID=FGFR3;PURPOSE=CNV;CNV_ID=FGFR3;CNV_HS=1
OCP1_CDK6_14:intron:CDK6:GENE_ID=CDK6;PURPOSE=CNV;CNV_ID=CDK6;CNV_HS=1

Here is two for loop code: 

my $i = 0;
my $j = 0;

for ( $i = 0; $i < @amplicon_exon; $i++ ) {

    for ( $j = 0; $j < @failedamplicons; $j++ ) {

        my $fail_amp = ( split /\./, $failedamplicons[$j] )[0];

        #print "the failed amp before match is $fail_amp\n";

        if ( index( $amplicon_exon[$i], $fail_amp ) != -1 ) {

            #print "the amplicon exon that matches $amplicon_exon[$i] and sample is $sample_id\n";
            print "the failed amp that matches $fail_amp and sample is $sample_id\n";

            my @parts = split /:/, $amplicon_exon[$i];
            my $exon_amp = $parts[1];

            next unless $parts[3] =~ /Hotspot/;    #includes only Hotspot amplicons
            my $gene_res   = $parts[2];
            my $depth      = ( split /\./, $failedamplicons[$j] )[1];
            my @total_amps = (
                $run_name, $sample_id, $gene_res, $depth, $fail_amp, $run_date, $matrix_status
            );

            my $lines = join "\t", @total_amps;

            push( @finallines, $lines );
        }
    }
}

Upvotes: 2

Views: 316

Answers (1)

stevieb
stevieb

Reputation: 9296

split and grep are your friends, as is the idiomatic approach to iterating over a list. Simply iterate over the first array, extract just the part you want to match on (by using split to split the element on a . character, then taking only the first entry), then using a regex, grep for that part of the string in the second array from the beginning of the element up to the ::

for my $elem (@failedamplicons){
    my $to_match = (split /\./, $elem)[0];
    if (my ($matched) = grep {$_ =~ /^\Q$to_match:/} @amplicon_exon){
        print "$matched\n";
    }        
}

Upvotes: 4

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