[DAS] DAS output

[Andrew Dalke]

Dmitriy V. Ryaboy:
Dmitriy V. Ryabo:
> Is there something wrong with this output?  Ensembl
> browser refuses to display it.  I am using the latest
> (Oct 31) version of LDAS.

I ran it against PyDAS.

>>> import DAS
>>> from DAS.dtds.strict import dasgff
>>> p = DAS.UsePOMParser("DAS.dtds.strict")
>>> s = """<?xml
        ... omitted for clarity
... """
>>> from cStringIO import StringIO
>>> f = StringIO(s)
>>> p.parse_using_dtd(f, "dasgff")
DAS.dtds.strict.dasgff.DASGFF()
>>>

This means the syntax is correct, according to the DTD I'm using

I then tested it against the 'dascheck' code, with a few changes
to make the following work (dascheck wasn't designed to work as
a module -- I'll fix that for future releases)

>>> dascheck.do_gff_check(None, "Dmitriy", (None, None), q)
WARNING: DSN 'Dmitriy'/types returns GFF with version '1.01', expected '1.0'
ERROR: DSN 'Dmitriy' 'types' request return a SEGMENT with id 'AC105394'
 which is missing the required 'version' attribute
ERROR: DSN 'Dmitriy' 'types' request return a SEGMENT with id 'AC105394.3.1.158127'
 which is missing the required 'version' attribute
>>>

I don't know if Ensembl's browser cares about these -- likely not.

					Andrew
					dalke@dalkescientific.com