Hello,

You are right! I forgot about that. Aren't regular expressions fun? And
please test it out, if you prefer your method or are just curious, I
didn't try it that way. There are usually a few ways to do the same
thing when using a regex.

But, I am glad that this helped a bit and good luck with the query,

Jen
Galaxy team

On 12/9/13 7:06 AM, 朱师云 wrote:
> Hi,
>
> It indeed helps.
> Your regular expression looks brief and more useful.
> BTW, a start of line (^) between [] and in the first location, for
> example, [^ATCGatcg] means a character not [ATCGatcg], which maybe not
> work in the tool SELECT.
>
> Thank you for your help!
>
> ------------------------------------------------------------------------
> Date: Mon, 9 Dec 2013 06:34:28 -0800
> From: j...@bx.psu.edu
> To: zhus...@msn.cn; galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] How to filter the sequences containing
> not[ATCG] character?
>
> Hello,
>
> If the data was in .fastqsanger format, you could use the tool
> "Manipulate FASTQ", but with .fasta, this is a good way.
>
> But watch your regular expression - test it out on a smaller set to
> make sure it is doing what you want. I see a "start of the line"
> character in the middle of your expression ("^"). I see why it could
> be working, with the prior expression being zero or more (*), but
> knowing what each character does is generally a good idea. The help on
> the tool is good as are many web sites, but this is simple. Also, you
> don't need the // slashes, just enter the expression.
>
> To get you started: I would use something like this, with the Select
> tool and "Matching":
>
> ^..*\t[ATCGatcg]+$
>
> (Only one dot is really required, this is just how I always do it.
> Adds a bit of a format sanity check into the filter).
>
> Hope this helps!
>
> Jen
> Galaxy team
>
>
> On 12/8/13 6:21 PM, 朱师云 wrote:
>
>     Hi Jen,
>     As the title, I have a [fasta] file that obtained from a [gtf] file,
>
>     >cuff102.1
>     atcgtaaagggcgat
>     >cuff103.1
>     gtcgttgactNNNNNNNNgtc
>
>     and I want to get the output like this to filter the sequences
>     that contain any not[ATCG] character?
>
>     >cuff102.1
>     atcgtaaagggcgat
>
>     I have a large of sequences to filter. I thought a way that
>     firstly convert the file to [interval] file, and secondly SELECT
>     the line not matching the patten /\t[ATCGatcg]*[^ATCGatcg]/.
>     Am I right? Or there is a one-step way ?
>
>
>
>
>
>     ___________________________________________________________
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>
> -- 
> Jennifer Hillman-Jackson
> http://galaxyproject.org

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
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