http://www.perlmonks.org?node_id=812874

Hena has asked for the wisdom of the Perl Monks concerning the following question:

Hi monks,

I'm trying to clean up a string which has some extra information in it for my situation. The string comes from a Samtools pileup. It's a representation of a single nucleotide from a multiple different sources (base reads column). My data in problem is following (note new lines added in order to prevent line being too long, they aren't really there :) )

.$.$G$.$.$C$.$.$.$G$.$,$,$,$.$.$.G,G,G...G,G...GG,.G.G...G.G....$.G..G +,........G....,GGGG.,,,..G...,,.G.G..G..G..G .G.GG..GG.G..,,G,,CG,G,GG..GG.$G.GGGG,,..GG...G.,G.GG.,G,G.$...,,.GGGG +GG.GCG..G,,G,.G..G,,,G,.GGGG.,..G...,,,,G,,G..GGGG A.,,,,,.+1GG.G.,,G,...G..GG,.G....+1G..GG..G,,G,,G.G,,.,,,.,,.CG.,,,,. +,..G.,,,.,.,,GGGGGG,,.....G..GGGGG.,.G,,GG.G..GG,, ,....,.,..,G.,.,,,.,,,,G,,,.,.,..,.,,,...GG,.,G.,G......,,,..,,....... +.,..,.,,.,...,,..,.,C,..,,,.,,,,,....,,..,,,.,.... .,.,,.,...,,.,,,-1a.,,,,,.,,,,,,..,..........,,,,,.,...,,.,,^],^].^],^ +],^].^],^F,^],^],^],^],


Now I want to do counting on bases and thus remove all extra information from it. I have regex like following s/\+([0-9]+)[ACGTNacgtn]{\1}//g; which unfortunately does't do anything. I'd like to know why? I would assume that quantifier cannot be a '\x' variable, but don't really know.

I can do the deed with
while (m/\+([0-9]+)[ACGTNacgtn]/g) { print "diff+: $1\n"; my $m = $1; s/\+[0-9]+[ACGTNacgtn]{$m}// }
But that's not quite so nice. I would be cool to be able to do it with one regex.

Help most appreciated,

Edit: Fixed the capture group in place where it should have been :).