perl scripts to load databases
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perl scripts to load databases
by Ryan Golhar
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Hi,
I noticed that in the documentation (http://gmod.org/wiki/GBrowse_Install_HOWTO), there is mention of bp_load_gff.pl / bp_bulk_load_gff.pl / and bp_fast_load_gff.pl to load data into a mysql database. Further down there is mention of using bp_seqfeature_load.pl for GFF3 files. Does that mean the first three perl scripts are for GFF2 only? I'm loading my GFF3 files (extension is .gff) with bp_load_gff.pl. Is that not correct? ------------------------------------------------------------------------------ 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: perl scripts to load databases
by Scott Cain-4
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Hi Ryan,
Ideally, you want to use the *load_gff.pl scripts with GFF2 to create a Bio::DB::GFF database, and you want to use bp_seqfeature_load.pl with GFF3 to create a Bio::DB::SeqFeature::Store database. While you can use *load_gff.pl with GFF3, the results will be less than optimal, particularly if you have features with multiple levels of parentage (like genes<-transcripts<-exons). In that case, it will be difficult or impossible to properly represent those multipart features. Scott On Wed, Oct 28, 2009 at 2:09 PM, Ryan Golhar <golharam@...> wrote: > Hi, > > I noticed that in the documentation > (http://gmod.org/wiki/GBrowse_Install_HOWTO), there is mention of > bp_load_gff.pl / bp_bulk_load_gff.pl / and bp_fast_load_gff.pl to load > data into a mysql database. > > Further down there is mention of using bp_seqfeature_load.pl for GFF3 files. > > Does that mean the first three perl scripts are for GFF2 only? I'm > loading my GFF3 files (extension is .gff) with bp_load_gff.pl. Is that > not correct? > > ------------------------------------------------------------------------------ > 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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