[Gusdev-gusdev] GBParser plugin issues

[Fidel S. <fi...@vb...>]

Folks,

I have used the GBParser plugin to upload all the mouse chromosomes and
ran into a couple of issues (actually, issue 2 I have seen with other data
as well).

1.  GBParser parsed 2 chromosome files incorrectly.
When I run the query:
select distinct chromosome, organism from dots.source where organism = 'Mus musculus'
chromosomes 11 and 16 are missing from the results.

Now, GBParser did not report any errors (gpparserFailures directory was
empty after completion and had not been modified since the uploading
started) and search for 'fail' or 'error' in the corresponding gbparser
ouput files turns up empty.  Chromosome info in the input *.gbk files
is there (in source features).  Searching for 'source' in the gbparser
output file again comes up empty.

Has anyone uploaded the same kind of chromosome files before?
Is what I have just described known to be a bug?

2.   GBParser fails on some feature qualifier types: mol_type, locus_tag,
and insertion_seq are the ones I have noticed.

This is more of a minor issue but also one that needs to be fixed.  I do not
know how long ago GenBank added these qualifier types but I know new feature
and qualifier types have been added for the latest release (138).

I am sorry to say I do not have time at the moment to fix these problems with
GBParser but I thought everyone should know.

Fidel