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,^],^],^],^],
[download]

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}// 
}
[download]

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 :).

---

---

• Are you posting in the right place? Check out Where do I post X? to know for sure.
• Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:

  <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>

• Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
• Want more info? How to link or How to display code and escape characters are good places to start.