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
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