Perhaps there is no good way to display such features in Jalview, but it might be preferable to skip such features, instead of aborting the parsing?
DBSW.aln (6.94 KB)
DBSW.gff (17.5 KB)
Hi Eric.
Eric Jain wrote:
Perhaps there is no good way to display such features in Jalview, but it might be preferable to skip such features, instead of aborting the parsing?
Actually, features with no start and end position are coped with from other formats - in particular its part of the DAS standard.
The gff file contains periods in the blank positions (Is that actually part of the standard or would they normally be left blank?). Jalview is trying to parse the field as a number and bailing out when that fails.
A couple of additional try/catch blocks fixed the problem - and this will be in the next release.
Jim
Jim Procter wrote:
Actually, features with no start and end position are coped with from other formats - in particular its part of the DAS standard.
The gff file contains periods in the blank positions (Is that actually part of the standard or would they normally be left blank?).
The gff spec doesn't seem to have any examples with unknown positions, but in general they do put dots in empty fields...
Jalview is trying to parse the field as a number and bailing out when that fails.
A couple of additional try/catch blocks fixed the problem - and this will be in the next release.
Great, thanks!