rbrusk1 at wave.home.com
Wed Apr 22 12:27:45 EST 1998
I've had to deal with this general problem before. The key fact is that
there is not generally any one program/script around to convert data
from a particular source into a particular ACEDB database. The reason
for this is that the structure (syntax/sematics) of the data must be
mapped onto the database schema (ACEDB "models"). Some general tools for
this may be available, but I find that often the best thing is to learn
(the basics of) a general utility scripting language like perl then
tackle the problem yourself.
1. Write down all the input data attribute fields. Organise them
into definable objects (i.e. "Locus", "Clone", "Sequence" etc)
2. Review your ACEDB models. Attempt to map source data attributes
onto your existing ACEDB model/tags. Add new tags if necessary.
"Read models" into your ACEDB database.
3. Write a perl script which inputs your source data, pattern
matches or parses the input into its attributes, then
write out .ace file lines corresponding to the mapped tags.
4. Read in the data.
If you give me a more accurate idea of precisely what LLNL data you wish
to input into ACEDB (URL?) and precisely what ACEDB models you using,
then perhaps I can advise you on this task, or we can locate existing
scripts (at Sanger, etc.) which might do the task.
Richard Bruskiewich (rbrusk at octogene.medgen.ubc.ca)
Dept. of Medical Genetics
University of British Columbia
Siddharth E Fernandes wrote:
> Dr. Matthews,
> I'm sorry for the ambiguity of my message. I wanted to take text
> data from the web and convert it onto ACEDB format. I am not on the
> bionet acedb newsgroup/mailing-list. Please tell me how to subscribe to
> this list. Thank you for your time.
> Siddharth Fernandes
> > Hi Siddharth,
> > I'm not exactly sure what you mean by "plate location information", but
> > maybe the Probe_Grid feature would help you? There's no help about
> > this in the ACEDB Documentation Library, and I've never used it myself.
> > I'll forward your message to the bionet acedb newsgroup/mailing-list.
> > I'm sure there must be someone on the list who's been working on the same
> > problem.
> > (If you aren't already subscribed to this list, let me know and I'll tell
> > you how.)
> > - Dave
> > > Subject: Re: ACEDB
> > > To: matthews at greengenes.cit.cornell.edu (Dave Matthews)
> > > Date: Mon, 20 Apr 1998 14:23:15 -0400 (EDT)
> > > From: "Siddharth E Fernandes" <siddhart at seas.upenn.edu>
> > >
> > > Dr. Matthews,
> > >
> > > I would like to thank you and you colleagues for the work you
> > > have done with the ACEDB documentation library page. It is quite helpful.
> > > I am curretly trying to export plate location information from
> > > text files in the LLNL homepage. I was wondering which programs I should
> > > utilize in order to produce a display from text data in ACEDB. I was
> > > considering using the text convert program (Perl Based) made available
> > > from your page. Thank you for your time.
> > >
> > > Siddharth Fernandes
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