Sorry, I was not sure if listserver will strip my small but gziped attachments or not, therefore played safe.
Darek Kedra --- On Fri, 3/5/10, Scott Cain <[email protected]> wrote: > From: Scott Cain <[email protected]> > Subject: Re: [apollo] loading gff3 CDS into apollo problem > To: "dar ked" <[email protected]> > Cc: "apollo Mailing List" <[email protected]> > Date: Friday, March 5, 2010, 12:47 PM > Hi Darek, > > Always reply to the list, as I can't help you with this > error; I'm a > GFF person, not an Apollo developer. Perhaps Ed or > someone else can > help you with this. > > Scott > > > On Fri, Mar 5, 2010 at 3:37 PM, dar ked <[email protected]> > wrote: > > Dear Scott, > > > > thank you for such prompt answer. > > I am sorry seems that I posted the previous version of > the file. > > This time I believe it should have just tabs. > > > > I am getting a different error (see attachment) but > still Apollo will not load it. > > > > Best wishes, > > > > 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: "dar ked" <[email protected]> > >> Cc: [email protected] > >> Date: Friday, March 5, 2010, 10:50 AM > >> Hi Darek, > >> > >> It looks like you have spaces rather than tabs > between most > >> of your > >> columns. GFF3 must have 9 tab delimited columns, > but > >> I think you only > >> have tabs between columns 8 and 9, whereas the > rest of the > >> columns are > >> separated by spaces. > >> > >> Scott > >> > >> > >> On Fri, Mar 5, 2010 at 1:32 PM, dar ked <[email protected]> > >> 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) > >> > > >> > > >> > > >> > > >> > > >> > > >> > > _______________________________________________ > >> > 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 > >> > > > > > > > > > > -- > ------------------------------------------------------------------------ > 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
