[Bioperl-l] How does '-alphabet' help? Is there any function which could remove "wrong" characters?

[Vasily Aushev]

well, then it should be rather something like $text =~
s/[^ATCGYRWSKMDVHBXNatcgyrwskmdvhbxn]//g; as ambiguous codes also make
valid sequence.


On Sun, Oct 13, 2013 at 7:35 AM, Jing Yu <logust79 at googlemail.com> wrote:

> I guess you can pretreat the line with something like $text =~
> s/[^ATCGatcg]//g;
>
> On 13 Oct 2013, at 11:24, Vasily Aushev <vaushev at gmail.com> wrote:
>
> well, in this particular case, this is the format of input file which I
> can't change: it is not Fasta format but just the sequence in one (first)
> line of the file.
> But I am interested in more general question - is there a function which
> removes all invalid characters from the string.
>
>