From: Scott C. <sc...@sc...> - 2009-11-09 16:49:35
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Hi Jim and Karen, It never occurred to me to use gene_component_region (who knows, maybe it didn't exist when the genbank2gff3 script was written :-) I'm looking at it know and hoping it will be an easy change. Scott On Mon, Nov 9, 2009 at 11:25 AM, Karen Eilbeck <kei...@ge...> wrote: > Hi Jim, > I think the converter is mapping the term misc_feature to region, as all it > can tell from the name is that its a region. I have not seen the code, but I > am assuming it has a hash to map between the features. > Then the converter is also recognizing that this misc_feature belongs to a > gene, so it put that relationship in, which then causes the validator to > barf because there is no relationship between region and gene in the > ontology. > Now I get it. > > One thing you could do is post process your gff3 file to update those > particular regions to be gene_component_region > You could also let someone at bioperl know. > > --K > > > On 11/9/09 9:14 AM, "Jim Hu" <ji...@ta...> wrote: > > Hi Karen, > > For the first question. There are cases where the BioPerl converter gives > things like this. The Genbank features are: > > gene 32225..33782 > /gene="Sv prime" > /locus_tag="P1_gp001" > /db_xref="GeneID:2777492" > misc_feature 32225..33782 > /gene="Sv prime" > /locus_tag="P1_gp001" > /standard_name="Sv prime" > /function="encodes carboxy-terminal moiety of tail > fiber > protein gpS prime in C(-) phage, expressed when its > sequence is in (-) orientation" > > > NC_005856 GenBank gene 32225 33782 . + . > ID=Sv prime;Dbxref=GeneID:2777492;gene=Sv prime;locus_tag=P1_gp001 > NC_005856 GenBank region 32225 33782 . + . > Parent=Sv prime;function=encodes carboxy-terminal moiety of tail fiber > protein gpS prime in C(-) phage%2C expresse\ > > So, here, the second line in the GFF is a region of a gene. But the > validator complains. > > In most other cases, regions just have coordinates and no parent features, > so I guess those are OK. > > Jim > > On Nov 5, 2009, at 3:34 PM, Karen Eilbeck wrote: > > > Hi Jim, > I’m not sure I understand the first question. What are the parent > relationships? > The second, a chromosome is a kind of region because it has a start and an > end coordinate, that are separated by at least 1 base. > > --K > > On 11/5/09 1:46 PM, "Jim Hu" <ji...@ta...> wrote: > > > > I'm confused about the usage of the term "region" > > The bp_genbank2gff3 script has given us lots of features that are tagged as > regions with parent relationships that the validator doesn't like. Some of > them have genes as parents, for example. I think the converter is using > region for the Genbank misc_feature. > > Should these be something else? Why is region a parent of chromosome? > > Thanks! > > Jim > > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. > http://p.sf.net/sfu/bobj-july_______________________________________________ > SOng-devel mailing list > SOn...@li... > https://lists.sourceforge.net/lists/listinfo/song-devel > > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > SOng-devel mailing list > SOn...@li... > https://lists.sourceforge.net/lists/listinfo/song-devel > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |