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 :) )
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
Help most appreciated,
Edit: Fixed the capture group in place where it should have been :).
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
But that's not quite so nice. I would be cool to be able to do it with one regex.while (m/\+([0-9]+)[ACGTNacgtn]/g) { print "diff+: $1\n"; my $m = $1; s/\+[0-9]+[ACGTNacgtn]{$m}// }
Help most appreciated,
Edit: Fixed the capture group in place where it should have been :).
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Replies are listed 'Best First'. | |
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Re: Regex fun
by JavaFan (Canon) on Dec 15, 2009 at 14:26 UTC | |
by Hena (Friar) on Dec 15, 2009 at 14:43 UTC | |
Re: Regex fun
by moritz (Cardinal) on Dec 15, 2009 at 14:28 UTC | |
Re: Regex fun
by AnomalousMonk (Archbishop) on Dec 15, 2009 at 15:43 UTC | |
Re: Regex fun
by JadeNB (Chaplain) on Dec 15, 2009 at 17:58 UTC | |
by Hena (Friar) on Dec 16, 2009 at 07:51 UTC | |
by JadeNB (Chaplain) on Dec 16, 2009 at 08:22 UTC | |
by Hena (Friar) on Dec 16, 2009 at 10:18 UTC | |
by JavaFan (Canon) on Dec 16, 2009 at 10:54 UTC | |
| |
by JadeNB (Chaplain) on Dec 16, 2009 at 15:57 UTC | |
Re: Regex fun
by ikegami (Patriarch) on Dec 15, 2009 at 20:39 UTC | |
by JadeNB (Chaplain) on Dec 15, 2009 at 21:08 UTC | |
by ikegami (Patriarch) on Dec 15, 2009 at 21:27 UTC | |
by JadeNB (Chaplain) on Dec 15, 2009 at 21:59 UTC | |
by ikegami (Patriarch) on Dec 15, 2009 at 22:22 UTC | |
| |
Re: Regex fun
by JadeNB (Chaplain) on Dec 15, 2009 at 19:01 UTC | |
by JavaFan (Canon) on Dec 15, 2009 at 19:40 UTC | |
by JadeNB (Chaplain) on Dec 15, 2009 at 20:22 UTC | |
by ikegami (Patriarch) on Dec 15, 2009 at 20:30 UTC | |
by JavaFan (Canon) on Dec 15, 2009 at 22:13 UTC | |
by JadeNB (Chaplain) on Dec 15, 2009 at 22:41 UTC | |
| |
Re: Regex fun
by Hena (Friar) on Dec 15, 2009 at 14:48 UTC | |
Re: Regex fun
by Anonymous Monk on Dec 15, 2009 at 14:33 UTC |
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