[Biopython] Another warning of "missing dtd file"

蔡火胜 hxcan at stupidbeauty.com
Sun May 29 07:18:22 UTC 2011


 /usr/lib/python2.6/site-packages/Bio/Entrez/Parser.py:495: UserWarning:
Unable to load DTD file bookdoc_110101.dtd.

Bio.Entrez uses NCBI's DTD files to parse XML files returned by NCBI Entrez.
Though most of NCBI's DTD files are included in the Biopython distribution,
sometimes you may find that a particular DTD file is missing. While we can
access the DTD file through the internet, the parser is much faster if the
required DTD files are available locally.

For this purpose, please download bookdoc_110101.dtd from

http://www.ncbi.nlm.nih.gov/entrez/query/DTD/bookdoc_110101.dtd

and save it either in directory

/usr/lib/python2.6/site-packages/Bio/Entrez/DTDs

or in directory

/Data/.biopython/Bio/Entrez/DTDs

in order for Bio.Entrez to find it.

Alternatively, you can save bookdoc_110101.dtd in the directory
Bio/Entrez/DTDs in the Biopython distribution, and reinstall Biopython.

Please also inform the Biopython developers about this missing DTD, by
reporting a bug on http://bugzilla.open-bio.org/ or sign up to our mailing
list and emailing us, so that we can include it with the next release of
Biopython.

Proceeding to access the DTD file through the internet...

warnings.warn(message)




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