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I'm trying to capture the start and end values. With a simple file such as:

Regex used: /^$RE{num}{real}\s+(\d+)\s+\.\.\s+(\d+)\s*/

>hsa_circ_0075116|chr5:175956288-175956388-|NM_014901|RNF44  FORWARD
-4.6      12 ..      35   xxxxGTGTGTGGTCT          GC TTCAGTGACTTCGAGG
+CGCG GC           AGCTGCTCCGAGTCC
-5.5      11 ..      36   xxxxxGTGTGTGGTC         TGC TTCAGTGACTTCGAGG
+CGCG GCA          GCTGCTCCGAGTCCT

[download]

I am able to capture the start and end values:

Dumper:
$VAR1 = 'hsa_circ_0075116|chr5:175956288-175956388-|NM_014901|RNF44  F
+ORWARD';
$VAR2 = [
          {
            'end' => '35',
            'start' => '12'
          },
          {
            'end' => '36',
            'start' => '11'
          }

[download]

But when I make a slight amendment in the regex to account for the lines which begin with a whitespace such as:

New regex: /^(\s+)?$RE{num}{real}\s+(\d+)\s+\.\.\s+(\d+)\s*/ 
 ## addition of (\s+)? to the beginning
*\s*-5      56 ..      70   CTATGCCCCTTATTG               TATCTG GGG C
+AGATG               ATCGTCAAGTGAAGA

[download]

The start values become undefined:

$VAR125 = 'hsa_circ_0067224|chr3:128345575-128345675-|NM_002950|RPN1  
+FORWARD';
$VAR126 = [
            {
              'end' => '6',
              'start' => undef
            }

[download]
Are the brackets used for optional capture at the beginning of my regex confusing what is captured by my $start and $end variables?

Whole script so far:

#!/usr/bin/perl 
use strict;
use warnings;
use Data::Dumper;
use Regexp::Common qw /number/;

open my $hairpin_file, '<', "new_xt_spacer_results.hairpin", or die $!
+;

my %HoA_sequences;
my $curkey;

while (<$hairpin_file>){
    chomp;
    
    if (/^>(\w+\d+\|\w+:\d+-\d+[-|+]\|\w+\|\w+\s+\w+$)/){
        $curkey = $1;

    }elsif (my ($start, $end) =     
        /^(\s+)?$RE{num}{real}\s+(\d+)\s+\.\.\s+(\d+)\s*/ ) {

            die "value seen before header: '$_'"
                unless defined $curkey;
            push @{ $HoA_sequences{$curkey}}, 
                { start=>$start, end=>$end };
    }
    else { die "don't know how to parse: '$_'" }
    
    
}
print Dumper(%HoA_sequences);

[download]

In reply to Re^2: Making use of a hash of an array... by Peter Keystrokes
in thread Making use of a hash of an array... by Peter Keystrokes

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