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,
On 12/9/13 7:06 AM, 朱师云 wrote:
> 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; email@example.com
> Subject: Re: [galaxy-user] How to filter the sequences containing
> not[ATCG] character？
> 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":
> (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!
> 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,
> and I want to get the output like this to filter the sequences
> that contain any not[ATCG] character?
> 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 ?
> The Galaxy User list should be used for the discussion of
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> Jennifer Hillman-Jackson
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: