Hello,

I have a regex whose behavior doesn't match my expectations.

The input data looks like this:

. transcript_id "g29202.t1"; gene_id "g29202"; gene_name "G42051"; xloc "XLOC_053322"; cmp_ref "G42051.1"; class_code "c"; tss_id "TSS54758";

. transcript_id "g29205.t1"; gene_id "g29205"; xloc "XLOC_053323"; class_code "u"; tss_id "TSS54760";

. transcript_id "g29176.t1"; gene_id "g29176"; xloc "XLOC_053324"; class_code "u"; tss_id "TSS54761";

. transcript_id "g29178.t1"; gene_id "g29178"; gene_name "G42030"; xloc "XLOC_053326"; cmp_ref "G42030.1"; class_code "o"; tss_id "TSS54763";

The code below works fine: 
use warnings;
use strict;
my $usage = "perl select_bracker.pl [bracker gtf] [output id list]\n";
my $gfin = shift or die $usage;
my $output = shift or die $usage;
open(IN, '<', $gfin);
open(OUT, '>>', $output);
while (my $record = <IN>){
    $record =~ s/\R//g;
    if ($record =~ /^.*transcript_id "([^"]*).*class_code "([^"]*)/){
        my $trans = $1;
        my $class = $2;
        if($class eq 's' | $class eq 'x' | $class eq 'u'){
            print OUT "$trans\n";
        }
    }
}
close IN;
close OUT;

[download]

but if instead of if($class eq 's' | $class eq 'x' | $class eq 'u') I have  if('sxu' =~ /$class/g) then the script works fine for the first line with a particular '$class' value it reads, but if it has two adjacent lines with the same '$class' value, the regex doesn't match and the print loop doesn't run for the second line (eg line 3 of the example input). I don't understand this at all, so any help would be much appreciated! Alastair

In reply to strange behavior of regex by biologistatsea

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