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: jen@bx.psu.edu To: zhusy88@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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