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, ÖìʦÔÆ
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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