Hi Derek, There is a GFF3 validator on the WormBase dev server:
http://dev.wormbase.org/db/validate_gff3/validate_gff3_online Though it appears to be down at the moment... :-/ Scott On Fri, Mar 5, 2010 at 3:48 PM, dar ked <[email protected]> wrote: > Hello, > > it is not a big problem at the moment, I just wanted to make sure that > I am not doing something rather silly with gff3 file format preventing me > from using all features provided by Apollo (and possibly other programs down > the road). > > On the other hand it would be great to have some canonical set of GFFs files > to which format any of our scripts would strive to achieve. > > Would you recommend any simple command utility for gff3 format checking, say > prior to loading it into Apolo? > > Best, > > Darek Kedra > > --- On Fri, 3/5/10, Scott Cain <[email protected]> wrote: > >> From: Scott Cain <[email protected]> >> Subject: Re: [apollo] loadin gff3 CDS into apollo problem >> To: "Ed Lee" <[email protected]> >> Cc: "dar ked" <[email protected]>, [email protected] >> Date: Friday, March 5, 2010, 11:40 AM >> 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 > -- ------------------------------------------------------------------------ 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
