question?

semna

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Join Date: Apr 2010

Posts: 55
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#1

question?

12-17-2010, 02:19 AM

Hi
I have a file that has a one column like this:

ENSSSCG00000000005|ENSSSCT00000000006
ENSSSCG00000000005|ENSSSCT00000000006
ATXN10|ENSSSCT00000000009
ENSSSCG00000019685|ENSSSCT00000021280
LDOC1L|ENSSSCT00000000023
-
TSPO|ENSSSCT00000000035
ENSSSCG00000000032|ENSSSCT00000000034
ENSSSCG00000000032|ENSSSCT00000000034
TTLL1|ENSSSCT00000000037
TTLL1|ENSSSCT00000000037
TTLL1|ENSSSCT00000000037
TTLL1|ENSSSCT00000000037
How can I get rid of lines that start with ENS or those lines that after gene name has |EN.......? Actually I want to keep just gene names like in this example ATXN10,LDOC1L,
TSPO and TTLL1.
Anyone know how can I do that? Thanks for your help
Tags: None

Bruins

Member

Join Date: Feb 2010
Posts: 78

12-17-2010, 02:54 AM

Also considering your other, related post I think that perhaps it would be worth it for you to learn Perl and regular expressions. Since that is not going to cut it for you today, here's some sed for you, play around with it (I'm no guru). Hope that helps!

cheers

Code:

sed -e'
  s/|ens(.+?)//g,
  s/ens(.+?)|ens(.+?)//g
' inputfile.txt > output.txt

Code:

enssscg00000000005|ensssct00000000006
enssscg00000000005|ensssct00000000006
atxn10|ensssct00000000009
enssscg00000019685|ensssct00000021280
ldoc1l|ensssct00000000023
-
tspo|ensssct00000000035
enssscg00000000032|ensssct00000000034
enssscg00000000032|ensssct00000000034
ttll1|ensssct00000000037
ttll1|ensssct00000000037
ttll1|ensssct00000000037
ttll1|ensssct00000000037

pls use code tags

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