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
