returning matched element from array - perl

Question

I would like to return an element of an array if it matches a pattern represented by a scalar. I would like to avoid looping so I've tried the following method:
use List::Util 'first';
my $match = first { /$pattern/ } #list_of_strings;
$match variable is not returning a value, even though, I know it matches exactly one element in array. What am I doing wrong?
my #amplicon_exon = ();
open(TXT5, "$amplicon_exon");
while (<TXT5>){
my $file_line = $_;
$file_line =~ s/\s+\z//g;
push (#amplicon_exon, $file_line);
}
close(TXT5);
foreach (#amplicon_exon){
chop($_);
}
my #matrix_lines = ();
open(TXT5, "$matrixfile");
while (<TXT5>){
my $matrixlineentry = $_;
$matrixlineentry =~ s/\s+\z//g;
push (#matrix_lines, $matrixlineentry);
}
close(TXT5);
foreach (#matrix_lines){
chop($_);
}
my #failedamplicons = ();
for my $vcf_file ( #vcf_files ) {
$vcf_file =~ m|([^/]+)_annotated.vcf$| or die "Can't extract Sample ID";
my $sample_id = $1;
my #myuniquearray = ();
my #amplicon_array = ();
my $entire_matrix_header = $matrix_lines[0]; print "The matrix header is ".$entire_matrix_header."\n";
$entire_matrix_header =~ s/\s+\z//g;
my #matrix_headers = split (/\t/, $entire_matrix_header);
push #matrix_headers, "endoffile";
my $matrix_column_number = "";
for (0..#matrix_headers){
my $onco_matrix_header = $matrix_headers[$_];
$onco_matrix_header =~ s/\s+\z//g;
if ((length $onco_matrix_header > 0) && (index($sample_id, $onco_matrix_header) != -1)) {
$matrix_column_number = $_;
print "The matrixcolumnnumber is ".$matrix_column_number."\n";
}
}
#print " The matrixcolumnnumber is ".$matrixcolumnnumber."\n";
for (1..#matrix_lines-1){
my #matrix_values = split (/\t/, $matrix_lines[$_]);
if ( ($matrix_values[$matrix_column_number]<201) && ($matrix_values[$matrix_column_number]>-1) ) {
my $f_amp = $matrix_values[1];#if ( grep( /^$value$/, #array ) )
print Dumper($f_amp, \#amplicon_exon);
my $match = first { /$f_amp/ } #amplicon_exon; print "#############the match is $match\n";
my #parts = split /:/, $match;
my $exon_amp = $parts[1]; my $gene_res = $parts[2];
print "less than 200 exists";
my #total_amps = ($run_folder, $sample_id, $gene_res, $exon_amp, $matrix_values[$matrix_column_number], $f_amp);
my $failedamplicon = join "\t", #total_amps;
push (#failedamplicons, $failedamplicon);
}
}
for (0..#failedamplicons-1){
my $failedamplicons = $failedamplicons[$_];
open (MYFILE, ">>$failed_amps_output");##opens files with header and adds the rest of the lines.
print MYFILE $failedamplicons."\n";
close (MYFILE);
}
}
Sample data:
#amplicon_exon lines:
ON_MAP2K1_1:2:MAP2K1
OCP1_MAP2K1_1:3:MAP2K1
OCP1_MAP2K1_2:6:MAP2K1
$f_amp examples:
ON_MAP2K1_1
OCP1_MAP2K1_1
OCP1_MAP2K1_2
matrixfile
Gene Target barcode-1 barcode-2 barcode-3 barcode-4 barcode-5
MOTOR Focus_MTOR_1 22 786 123 456 456
JAK1 OCP1_JAK1_2 345 45 342 23 432
ALT OCP1_ALK_3 43 456 23 3 56

Answer 1

There is something wrong with part of the program that you haven't shown
Here is a short program that uses exactly the #amplicon_exon values that you have given as examples, and dumps the result of the first call for every value of $f_cmp. It works
Perhaps this will shake you from your insistence that you have done nothing wrong?
use strict;
use warnings 'all';
use List::Util 'first';
use Data::Dump;
# Using sample #amplicon_exon lines
my #amplicon_exon = qw/
ON_MAP2K1_1:2:MAP2K1
OCP1_MAP2K1_1:3:MAP2K1
OCP1_MAP2K1_2:6:MAP2K1
/;
# Using $f_amp examples:
for my $f_amp (qw/
ON_MAP2K1_1
OCP1_MAP2K1_1
OCP1_MAP2K1_2 / ) {
my $match = first { /$f_amp/ } #amplicon_exon;
dd $match;
}
output
"ON_MAP2K1_1:2:MAP2K1"
"OCP1_MAP2K1_1:3:MAP2K1"
"OCP1_MAP2K1_2:6:MAP2K1"
I'd risk £5 that your #matrix_values contains newlines