filling cvtermpath

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filling cvtermpath

Yuri Bendana-3
What's the recommended way to fill the cvtermpath table?  I learned about the make-cvtermpath.pl from a recent posting so I guess it's still actively used.  However, the version in svn has a couple of bugs due to hardcoded values and hasn't been updated in a while.  It seems to work ok after fixing it.  Then I also see the stored procedure fill_cvtermpath. But I also saw this thread recommending the equivalent of obo2linkfile:


I had assumed that the cvtermpath would be filled automatically when doing 'make ontologies' but this doesn't happen for me.  Is this the right behavior?

thanks,

yuri


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Re: filling cvtermpath

Naama Menda
hi Yuri,

make_cvtermpath.pl is very old (and should be removed from svn..)
You can use gmod_make_cvtermpath.pl in bin/cxgn/

http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/bin/cxgn/gmod_make_cvtermpath.pl?view=log

Let me know if this does not work for you!

As far as I know , 'make ontologies' does not fill the cvtermpath.

-Naama


Naama Menda
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On Fri, Aug 27, 2010 at 11:09 PM, Yuri Bendana <[hidden email]> wrote:
What's the recommended way to fill the cvtermpath table?  I learned about the make-cvtermpath.pl from a recent posting so I guess it's still actively used.  However, the version in svn has a couple of bugs due to hardcoded values and hasn't been updated in a while.  It seems to work ok after fixing it.  Then I also see the stored procedure fill_cvtermpath. But I also saw this thread recommending the equivalent of obo2linkfile:


I had assumed that the cvtermpath would be filled automatically when doing 'make ontologies' but this doesn't happen for me.  Is this the right behavior?

thanks,

yuri


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Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
Be part of this innovative community and reach millions of netbook users
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speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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