load both gff2 and gff3 into the same db?
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load both gff2 and gff3 into the same db?
by Lacey Sanderson-2
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Just wondering if it is possible to load both gff2 and gff3 files into
the same database? I have some old data that has been given to me in gff2 but I would like to generate all our new data in gff3... If not is there a conversion problam that any of you recommend? I hear there are some issues with converting between the two versions and was wondering if any of the converters handle these better than the others. Thanks! Lacey ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: load both gff2 and gff3 into the same db?
by Scott Cain-4
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Hi Lacey,
You can't load GFF2 and GFF3 into the same database, and there are no general purpose converters, as it is quite tricky to anticipate all of the strange things that people might have done in their GFF2 (if there were an easy way to convert them generally, we probably wouldn't have needed GFF3! :-) Typically though, in specific cases, it isn't to hard to convert to GFF3 with a simple perl script written for the set of files, or if the GFF2 was obtained elsewhere, someone may have already written a convert for that "flavor" of GFF2. For example, there are a few JGI converters out there. Scott On Mon, Oct 19, 2009 at 12:32 PM, Lacey Sanderson <las166@...> wrote: > Just wondering if it is possible to load both gff2 and gff3 files into > the same database? I have some old data that has been given to me in > gff2 but I would like to generate all our new data in gff3... > > If not is there a conversion problam that any of you recommend? I hear > there are some issues with converting between the two versions and was > wondering if any of the converters handle these better than the others. > > Thanks! > Lacey > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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