Question: Converting between old and new annotation packages?
0
gravatar for Jeff Gentry
11.4 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
Hi there ... Is it possible to directly convert an old style annotation package to the new SQLite *.db style packages without rebuilding from scratch? I didn't see anything when poking around and I'm guessing the answer ranges from "no" to "patches welcome" but figured it was worth a query. Thanks -J
annotation convert • 399 views
ADD COMMENTlink modified 11.4 years ago • written 11.4 years ago by Jeff Gentry3.9k
Answer: Converting between old and new annotation packages?
0
gravatar for Marc Carlson
11.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Jeff Gentry wrote: > Hi there ... > > Is it possible to directly convert an old style annotation package to the > new SQLite *.db style packages without rebuilding from scratch? I didn't > see anything when poking around and I'm guessing the answer ranges from > "no" to "patches welcome" but figured it was worth a query. > > Thanks > -J > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Jeff, The short answer is no. The slightly longer answer is that the new style of packages are much more complex than the old ones because they each contain an actual sqlite database. So you could convert from the new style package "down" into one of the older style packages by querying the database and saving the results as simple environments. But you cannot easily go in the other direction. We already support making new chip packages via SQLForge in the AnnotationDbi package for most major model organisms. What did you need this for? Marc
ADD COMMENTlink written 11.4 years ago by Marc Carlson7.2k
Answer: Converting between old and new annotation packages?
0
gravatar for Jeff Gentry
11.4 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
Hi Marc ... > The slightly longer answer is that the new style of packages are much > more complex than the old ones because they each contain an actual > sqlite database. So you could convert from the new style package "down" > into one of the older style packages by querying the database and saving > the results as simple environments. But you cannot easily go in the > other direction. Ah well, figured as much. > We already support making new chip packages via SQLForge in the > AnnotationDbi package for most major model organisms. What did you > need this for? I have a bunch of anno packages for custom spotted array chips from a few years back that I was looking to bring into the modern age, and in several cases would have to go track down the mapping files and such again ... so it seemed worth looking into if there was a way of moving from one to the other w/o doing just that. Its not a big deal, was just trying to figure out the path of least resistance.
ADD COMMENTlink written 11.4 years ago by Jeff Gentry3.9k
Jeff Gentry wrote: > Hi Marc ... > >> The slightly longer answer is that the new style of packages are much >> more complex than the old ones because they each contain an actual >> sqlite database. So you could convert from the new style package "down" >> into one of the older style packages by querying the database and saving >> the results as simple environments. But you cannot easily go in the >> other direction. > > Ah well, figured as much. > >> We already support making new chip packages via SQLForge in the >> AnnotationDbi package for most major model organisms. What did you >> need this for? > > I have a bunch of anno packages for custom spotted array chips from a few > years back that I was looking to bring into the modern age, and in several > cases would have to go track down the mapping files and such again ... so > it seemed worth looking into if there was a way of moving from one to the > other w/o doing just that. Its not a big deal, was just trying to figure > out the path of least resistance. Well, you can always get a simple map from your IDs to Entrez gene from your current package, and then use that as input, so you don't really need to go back to the originals (granted you may want to go back as things are likely to have changed since the mapping was done). But at least if you cannot recover files, you can still build something. best wishes Robert > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD REPLYlink written 11.4 years ago by rgentleman5.5k
> Well, you can always get a simple map from your IDs to Entrez gene > from your current package, and then use that as input, so you don't > really need to go back to the originals (granted you may want to go > back as things are likely to have changed since the mapping was done). > But at least if you cannot recover files, you can still build > something. That's a good point - if I come across something where I can't dig up the old info this might be the way to go. And another good point on the changes in maps anyways making it wise to just start anew anyways. Thanks -J
ADD REPLYlink written 11.4 years ago by Jeff Gentry3.9k
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