Re: Splitting only on internal pattern, not at start or end of string

All of the split solutions using look-arounds that have been posted so far have problems coping with Ns at the beginning or end of the string. If you want to use split I think the simplest approach would be to combine it with grep and length, splitting on one or more Ns without any look-arounds.

$ perl -E '
> $seq = q{NNACGTNNNACGTNACGTNN};
> say for grep length, split m{N+}, $seq;'
ACGT
ACGT
ACGT
$
[download]

I hope this is of interest.

Cheers,

JohnGG

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Re^2: Splitting only on internal pattern, not at start or end of string by Anonymous Monk on Jan 16, 2014 at 14:27 UTC
Thanks everyone, this is all very helpful, and very much a great learning experience for me. I see now that indeed the first solution will remove characters I want to keep, so I will update my script as necessary.	[reply]
Re^2: Splitting only on internal pattern, not at start or end of string by Anonymous Monk on Jan 16, 2014 at 15:13 UTC
One wonders if BiologySwede had not intended to not keep the leading/trailing N's, or not?	[reply]