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                                          
___________________________________________________________
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