use strict;
my $str = 'chr1 hg19_refFlat exon 44160380 44160565 0.000000 + . gene_id "KDM4A"; transcript_id "KDM4A";
chr1 hg19_refFlat exon 19563636 19563732 0.000000 - . gene_id "EMC1"; transcript_id "EMC1";
chr1 hg19_refFlat exon 52870219 52870551 0.000000 + . gene_id "PRPF38A"; transcript_id "PRPF38A";
chr1 hg19_refFlat exon 53373540 53373626 0.000000 - . gene_id "ECHDC2"; transcript_id "ECHDC2_dup2";
chr1 hg19_refFlat exon 11839859 11840067 0.000000 + . gene_id "C1orf167"; transcript_id "C1orf167";
chr1 hg19_refFlat exon 29037032 29037154 0.000000 + . gene_id "GMEB1"; transcript_id "GMEB1";
chr1 hg19_refFlat exon 103356007 103356060 0.000000 - . gene_id "COL11A1"; transcript_id "COL11A1";';
my $regex = qr/\bexon\s+(\d+)\b.*?\s+gene_id\s+"([^"]*)"/mp;
if ( $str =~ /$regex/g ) {
print "Whole match is ${^MATCH} and its start/end positions can be obtained via \$-[0] and \$+[0]\n";
# print "Capture Group 1 is $1 and its start/end positions can be obtained via \$-[1] and \$+[1]\n";
# print "Capture Group 2 is $2 ... and so on\n";
}
# ${^POSTMATCH} and ${^PREMATCH} are also available with the use of '/p'
# Named capture groups can be called via $+{name}
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html