I fixed a syntax error, added a leading '>' character to your input string, used
perltidy to neaten up the indentation, added the strictures and used the DATA handle to create a self-contained, runnable example.
use strict;
use warnings;
my %loc;
while (<DATA>) {
chomp;
if (/^>(\w+)\s\w+\=(chr\w+)\:(\d+)\-(\d+).*\+(.*)/) {
$loc{$1} = "$2:$3:$4:$5";
print $loc{$1} . "\n";
}
}
__DATA__
>hg19_ensGene_ENST00000237247 range=chr1:67208779-67210057 5'pad=0 3'p
+ad=0 strand=+ repeatMasking=none
Prints:
chr1:67208779:67210057: repeatMasking=none
Also, there is no reason to back-whack
= or
: or
- in your regex. This will also work:
if (/^>(\w+)\s\w+=(chr\w+):(\d+)-(\d+).*\+(.*)/) {
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