Haha, yeah, also what Scott said about the file format ;)
Cheers,
Ed
On Fri, 5 Mar 2010, Scott Cain wrote:
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)
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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