Hi Ed, That is problematic for the Chado GFF3 loader as well. The (non-optimal) way that I solved it was to require that a file contain only analysis results or only "annotations" (ie, not analysis results) and then telling the loader when it is started which type of data it contains. Perhaps you could take a similar approach, or we could decide on a standard and have it added to the GFF3 spec (that could take a while though!)
Scott On Fri, Mar 5, 2010 at 2:23 PM, Ed Lee <[email protected]> wrote: > Hi Darek, > > Unfortunately, I don't think there's a guaranteed way in GFF3 to > point that a feature is from an analysis result (rather than > an annotation). "match" guarantees that a feature isn't an annotation > but an analysis result, so we can display data in the appropriate > track. You can still track the source of the analysis through the > source column. > > Cheers, > Ed > > On Fri, 5 Mar 2010, dar ked wrote: > >> Hello, >> >> I am having a problem with loading gff3-like(?) file into Apollo >> 1.11.3. Changing "CDS" to "match" solves the problem, but making the >> output of this gene prediction program compatible with Apollo would be much >> more sensible. >> >> Below is uuencoded small gff3 file. >> >> If anybody can point to incompatible things / provide me with >> version acceptable by Apollo that will be very helpful. >> >> Sincerely yours, >> >> Darek Kedra >> PS the error is: >> Exception in thread "Thread-55" >> apollo.dataadapter.NonFatalDataAdapterException: Invalid number of columns >> at apollo.dataadapter.gff3.GFF3Entry.parseData(GFF3Entry.java:523) >> at apollo.dataadapter.gff3.GFF3Entry.<init>(GFF3Entry.java:72) >> >> >> begin 644 genecaller_ecol.gff3 >> M(R-G9F8M=F5R<VEO;B`@,PHC(U-E<75E;F-E.B`Q("@T-C,Y-C<U(&)P*3H@ >> M3D-?,#`P.3$S(",@17-C:&5R:6-H:6...@8v]l:2!S='(N($LM,3(@<W5B<W1R >> M+B!-1S$V-34L"F-O;7!L971E(&=E;F]M92X*3D-?,#`P.3$S("`@("`@(&=E >> M;F5C86QL97)?=C(N,#`@($-$4R`@("`@,S,W("`@("`R-SDY("`@(#,S."XW >> M("`...@*r`@("`@("`P"4E$/3%?,3MP87)T:6%L/3`P.W1Y<&4]051'.W-C;W)E >> M/3,R,BXQ-SMR8G-?;6]T:68]1T=!1R]'04='.W)B<U]S<&%C97(]-2TQ,&)P >> M.V-S8V]R93TS,C(N,3<[<W-C;W)E/3$V+C4T.W)S8V]R93TQ,2XR-#MU<V-O >> M<F4],2XS-3MT<V-O<F4],RXY-0I.0U\P,#`Y,3,@("`@("`...@9v5n96-a;&QE >> M<E]V,BXP,"`...@0t13("`@("`R.#`Q("`@(#,W,S,@("`@,3$W+CD@("`K("`@ >> M("`@(#`)240],5\R.W!A<G1I86P],#`[='EP93U!5$<[<V-O<F4]-#,W+C0T >> M.W)B<U]M;W1I9CU!1T=!1SMR8G-?<W!A8V5R/34M,3!B<#MC<V-O<F4].3<N >> M-#8[<W-C;W)E/3(P+C0R.W)S8V]R93TQ-"XX-SMU<V-O<F4],"XS-#MT<V-O >> M<F4],RXY-0I.0U\P,#`Y,3,@("`@("`...@9v5n96-a;&QE<E]V,BXP,"`...@0t13 >> M("`@("`S-S,T("`@(#4P,C`@("`@,3DU+C$@("`K("`@("`@(#`)240],5\S >> M.W!A<G1I86P],#`[='EP93U!5$<[<V-O<F4]-C0X+C8Q.W)B<U]M;W1I9CU' >> M1T$O1T%'+T%'1SMR8G-?<W!A8V5R/34M,3!B<#MC<V-O<F4],3DP+C<T.W-S >> M8V]R93TT+C,V.W)S8V]R93TR+CDX.W5S8V]R93TM,RXX-#MT<V-O<F4],RXY >> M-0I.0U\P,#`Y,3,@("`@("`...@9v5n96-a;&QE<E]V,BXP,"`...@0t13("`@("`U >> M,C,T("`@(#4U,S`@("`...@."XP("`@("`K("`@("`@(#`)240],5\T.W!A<G1I >> M86P],#`[='EP93U'5$<[<V-O<F4]-C4Q+C0Y.W)B<U]M;W1I9CU!1T=!1SMR >> M8G-?<W!A8V5R/34M,3!B<#MC<V-O<F4],"XT-3MS<V-O<F4]-RXU-SMR<V-O >> C<F4],30N.#<[=7-C;W)E/2TP+C`T.W1S8V]R93TM-BXV,`H` >> ` >> end >> >> >> >> >> _______________________________________________ >> apollo mailing list >> [email protected] >> http://mail.fruitfly.org/mailman/listinfo/apollo >> >> > _______________________________________________ > apollo mailing list > [email protected] > http://mail.fruitfly.org/mailman/listinfo/apollo > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
