|

Bio-Informatics

»

Generic Model Organism System Database

»

Losing IDs with bp_seqfeature_load

View: New views

3 Messages — Rating Filter: Alert me

	Losing IDs with bp_seqfeature_load by Andrew.Spriggs :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi, I'm running Gbrowse2, using Bio::DB::SeqFeature::Store with the MySQL backend and I load some GFF3 data using bp_seqfeature_load.pl that looks, for example, like this- Chr1 MSU_osa1r6 gene 10218 11435 . + . ID=13101.t00002;Note=expressed%20protein;Name=LOC_Os01g01019 Chr1 MSU_osa1r6 mRNA 10218 11435 . + . ID=13101.m00003;Parent=13101.t00002;Name=LOC_Os01g01019.1 Chr1 MSU_osa1r6 five_prime_utr 10218 10797 . + . Parent=13101.m00003 Chr1 MSU_osa1r6 CDS 10798 11060 . + 0 Parent=13101.m00003 Chr1 MSU_osa1r6 CDS 11152 11317 . + 2 Parent=13101.m00003 Chr1 MSU_osa1r6 three_prime_utr 11318 11435 . + . Parent=13101.m00003 I display it with the gene glyth and it all displays as it should and that side of it is great. However, searching for genes based on their IDs turns up no results and when I use the BatchDumper plugin to pull the GFF back out, this gene now looks like this- Chr1 MSU_osa1r6 gene 10218 11435 . + . Name=LOC_Os01g01019;ID=45;Note=expressed%20protein Chr1 MSU_osa1r6 mRNA 10218 11435 . + . Name=LOC_Os01g01019.1;Parent=45;ID=46 Chr1 MSU_osa1r6 five_prime_utr 10218 10797 . + . Parent=46;ID=47 Chr1 MSU_osa1r6 CDS 10798 11060 . + 0 Parent=46;ID=48 Chr1 MSU_osa1r6 CDS 11152 11317 . + 2 Parent=46;ID=49 Chr1 MSU_osa1r6 three_prime_utr 11318 11435 . + . Parent=46;ID=50 Chr1 MSU_osa1r6 mRNA 10218 11435 . + . Sequence LOC_Os01g01019.1 As you can see, the proper IDs have been replaced by incremental integers. Have I missed something which has caused this problem? Possibly related, clicking on the gene, rather than showing it's sequence and details or anything, just shows- "LOC_Os01g01019 Details Requested feature not found in database." Any help would be appreciated. Thanks, Andrew ------------------------------------------------------------------------------ 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
	Re: Losing IDs with bp_seqfeature_load by Lincoln Stein-3 :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi, The IDs are used during loading only. If you want a stable searchable identifier, use it as the Name or Alias field. Lincoln On Tue, Oct 27, 2009 at 2:55 AM, <Andrew.Spriggs@...> wrote: Hi, I'm running Gbrowse2, using Bio::DB::SeqFeature::Store with the MySQL backend and I load some GFF3 data using bp_seqfeature_load.pl that looks, for example, like this- Chr1 MSU_osa1r6 gene 10218 11435 . + . ID=13101.t00002;Note=expressed%20protein;Name=LOC_Os01g01019 Chr1 MSU_osa1r6 mRNA 10218 11435 . + . ID=13101.m00003;Parent=13101.t00002;Name=LOC_Os01g01019.1 Chr1 MSU_osa1r6 five_prime_utr 10218 10797 . + . Parent=13101.m00003 Chr1 MSU_osa1r6 CDS 10798 11060 . + 0 Parent=13101.m00003 Chr1 MSU_osa1r6 CDS 11152 11317 . + 2 Parent=13101.m00003 Chr1 MSU_osa1r6 three_prime_utr 11318 11435 . + . Parent=13101.m00003 I display it with the gene glyth and it all displays as it should and that side of it is great. However, searching for genes based on their IDs turns up no results and when I use the BatchDumper plugin to pull the GFF back out, this gene now looks like this- Chr1 MSU_osa1r6 gene 10218 11435 . + . Name=LOC_Os01g01019;ID=45;Note=expressed%20protein Chr1 MSU_osa1r6 mRNA 10218 11435 . + . Name=LOC_Os01g01019.1;Parent=45;ID=46 Chr1 MSU_osa1r6 five_prime_utr 10218 10797 . + . Parent=46;ID=47 Chr1 MSU_osa1r6 CDS 10798 11060 . + 0 Parent=46;ID=48 Chr1 MSU_osa1r6 CDS 11152 11317 . + 2 Parent=46;ID=49 Chr1 MSU_osa1r6 three_prime_utr 11318 11435 . + . Parent=46;ID=50 Chr1 MSU_osa1r6 mRNA 10218 11435 . + . Sequence LOC_Os01g01019.1 As you can see, the proper IDs have been replaced by incremental integers. Have I missed something which has caused this problem? Possibly related, clicking on the gene, rather than showing it's sequence and details or anything, just shows- "LOC_Os01g01019 Details Requested feature not found in database." Any help would be appreciated. Thanks, Andrew ------------------------------------------------------------------------------ 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 -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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
	Re: Losing IDs with bp_seqfeature_load by Andrew.Spriggs :: Rate this Message: Reply to Author \| View Threaded \| Show Only this Message Hi Lincoln, Thanks for that help. I hadn't realised that about the ID field. Use of the Alias tag allowed me to make the genes searchable by both of their names. I still have a remaining problem- clicking on the gene, rather than showing it's details or anything, just shows- "LOC_Os01g01019 Details Requested feature not found in database." The uri it goes to is like: ?ref=Chr1;start=10218;end=11435;name=LOC_Os01g01019;class=Sequence;feature_id=45;db_id=general Any idea why this isn't working? (I'll actually be changing it to an external link, but I'm still curious as to why the automatic internal link isn't working at the moment and if that's a problem) Thanks, Andrew From: Lincoln Stein [mailto:lincoln.stein@...] Sent: Wednesday, 28 October 2009 12:29 AM To: Spriggs, Andrew (PI, Black Mountain) Cc: gmod-gbrowse@... Subject: Re: [Gmod-gbrowse] Losing IDs with bp_seqfeature_load Hi, The IDs are used during loading only. If you want a stable searchable identifier, use it as the Name or Alias field. Lincoln On Tue, Oct 27, 2009 at 2:55 AM, <Andrew.Spriggs@...> wrote: Hi, I'm running Gbrowse2, using Bio::DB::SeqFeature::Store with the MySQL backend and I load some GFF3 data using bp_seqfeature_load.pl that looks, for example, like this- Chr1 MSU_osa1r6 gene 10218 11435 . + . ID=13101.t00002;Note=expressed%20protein;Name=LOC_Os01g01019 Chr1 MSU_osa1r6 mRNA 10218 11435 . + . ID=13101.m00003;Parent=13101.t00002;Name=LOC_Os01g01019.1 Chr1 MSU_osa1r6 five_prime_utr 10218 10797 . + . Parent=13101.m00003 Chr1 MSU_osa1r6 CDS 10798 11060 . + 0 Parent=13101.m00003 Chr1 MSU_osa1r6 CDS 11152 11317 . + 2 Parent=13101.m00003 Chr1 MSU_osa1r6 three_prime_utr 11318 11435 . + . Parent=13101.m00003 I display it with the gene glyth and it all displays as it should and that side of it is great. However, searching for genes based on their IDs turns up no results and when I use the BatchDumper plugin to pull the GFF back out, this gene now looks like this- Chr1 MSU_osa1r6 gene 10218 11435 . + . Name=LOC_Os01g01019;ID=45;Note=expressed%20protein Chr1 MSU_osa1r6 mRNA 10218 11435 . + . Name=LOC_Os01g01019.1;Parent=45;ID=46 Chr1 MSU_osa1r6 five_prime_utr 10218 10797 . + . Parent=46;ID=47 Chr1 MSU_osa1r6 CDS 10798 11060 . + 0 Parent=46;ID=48 Chr1 MSU_osa1r6 CDS 11152 11317 . + 2 Parent=46;ID=49 Chr1 MSU_osa1r6 three_prime_utr 11318 11435 . + . Parent=46;ID=50 Chr1 MSU_osa1r6 mRNA 10218 11435 . + . Sequence LOC_Os01g01019.1 As you can see, the proper IDs have been replaced by incremental integers. Have I missed something which has caused this problem? Possibly related, clicking on the gene, rather than showing it's sequence and details or anything, just shows- "LOC_Os01g01019 Details Requested feature not found in database." Any help would be appreciated. Thanks, Andrew ------------------------------------------------------------------------------ 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 -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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