Perl script in miRanda microRNA data output

[kennerqq]

Hi all,

  I used miRanda software to predict the microRNA target from 3'UTR. It come
up with a large file which includes those "hits" and "no hits" lines. Since
it is too big to handle, i want to remove the "no hits" lines. I heard that
using a simple Perl Script can easily get rid of "no hits" lines in the
document. Unfortunately, I do not know how to use it. Does anybody have a
clue?

 Thanks a lot,

Ken
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[Morris, Chris (STFC,DL,CSE)]

You don't even need per perl. Just do:
    grep -v 'no hits' output.txt

____________________________________________
Chris Morris
chris.morris@...
Tel: [phone]  Fax: [phone]
Mobile: [phone]
http://pims.instruct-fp7.eu/ 
STFC, Daresbury Lab,  Daresbury,  Warrington,  UK,  WA4 4AD

> -----Original Message-----
> From: comp-bio-bounces@... [mailto:comp-bio-
> bounces@...] On Behalf Of kennerqq
> Sent: 28 September 2009 19:53
> To: comp-bio@...
> Subject: [Computational-biology] Perl script in miRanda microRNA data
output
>
> Hi all,
>
>   I used miRanda software to predict the microRNA target from 3'UTR.
It come
> up with a large file which includes those "hits" and "no hits" lines.
Since
> it is too big to handle, i want to remove the "no hits" lines. I heard
that
> using a simple Perl Script can easily get rid of "no hits" lines in
the
> document. Unfortunately, I do not know how to use it. Does anybody
have a
> clue?
>
>  Thanks a lot,
>
> Ken
> _______________________________________________
> Comp-bio mailing list
> Comp-bio@...
> http://www.bio.net/biomail/listinfo/comp-bio
--
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[Lyle Wiedeman]

It's also easy and sometimes faster to do with sed:

sed -e '/no hits/d' output.txt

        Lyle Wiedeman
        UC Irvine

-----Original Message-----
From: comp-bio-bounces@...
[mailto:comp-bio-bounces@...] On Behalf Of Morris, Chris
(STFC,DL,CSE)
Sent: Tuesday, September 29, 2009 3:44 AM
To: kennerqq; comp-bio@...
Subject: RE: [Computational-biology] Perl script in miRanda microRNA data
output

You don't even need per perl. Just do:
    grep -v 'no hits' output.txt

____________________________________________
Chris Morris
chris.morris@...
Tel: [phone]  Fax: [phone]
Mobile: [phone]
http://pims.instruct-fp7.eu/ 
STFC, Daresbury Lab,  Daresbury,  Warrington,  UK,  WA4 4AD

> -----Original Message-----
> From: comp-bio-bounces@... [mailto:comp-bio-
> bounces@...] On Behalf Of kennerqq
> Sent: 28 September 2009 19:53
> To: comp-bio@...
> Subject: [Computational-biology] Perl script in miRanda microRNA data
output
>
> Hi all,
>
>   I used miRanda software to predict the microRNA target from 3'UTR.
It come
> up with a large file which includes those "hits" and "no hits" lines.
Since
> it is too big to handle, i want to remove the "no hits" lines. I heard
that
> using a simple Perl Script can easily get rid of "no hits" lines in
the
> document. Unfortunately, I do not know how to use it. Does anybody
have a
> clue?
>
>  Thanks a lot,
>
> Ken
> _______________________________________________
> Comp-bio mailing list
> Comp-bio@...
> http://www.bio.net/biomail/listinfo/comp-bio
--
Scanned by iCritical.

_______________________________________________
Comp-bio mailing list
Comp-bio@...
http://www.bio.net/biomail/listinfo/comp-bio

_______________________________________________
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Comp-bio@...
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