[Bioperl-l] Bio ::seqIO ::tigr

Keith James kdj at sanger.ac.uk
Tue Jan 27 06:57:26 EST 2004

>>>>> "matthieu" == matthieu CONTE <m_conte at hotmail.com> writes:

    matthieu> I currently trying to use the Bio ::seqIO ::tigr module.
    matthieu> My objective is to download the whole rice genome form
    matthieu> Tigr ( adress below)and to integrate it in my BioSQL DB.
    matthieu> For this I am trying to convert the tigr format in swiss
    matthieu> format with the script below

This looks like a mismatch between the version of your XML data and
the DTD. However, it is hard to be sure without knowing the download
dates of your data and DTD. TIGR change the DTD fairly regularly and
although they aim to be backwards-compatible this does not always
occur (e.g. adding new mandatory attributes or elements). I find it is
good to download a new DTD each time, diff it against the previous one
and then archive it if there are any changes.

Looking at the their FTP site it seems that the XML files there have
this element. Look at your file - does the ASSEMBLY element have a
HEADER element with an AUTHOR_LIST element in it?



- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -

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