[BioPython] documentation issues

andrea rossi andrea at salilab.org
Thu Jan 27 15:56:26 EST 2005


Dear all,

I'm learning biopython and after a good start with the tutorial and
cookbok I ran into the genbank section (section 3.4). I think the
tutorial is really well written and very useful, but I couldn't make
work some of the genbank examples. For example when I run: 

    from Bio import GenBank

    gi_list = GenBank.search_for("Opuntia AND rpl16")
    print " gi_list[0] ", gi_list[0]

I get the message:

    gi_list[0]  Error: Sequence Viewer does not have any Presentations
for code='uilist_text'

instead of:

   ['6273291', '6273290', '6273289', '6273287', '6273286', '6273285',
'6273284']

Before, I ran into other problems such as bug 1740 and revison 1.3 to
Bio/Eutils/parse.py.

What is the best place to continue my exploration of biopython? The
scripts in Tests/ such as test_genbank.py? Or the one in
Scripts/GenBank/? Or again the one in Doc/examples? Or the one in
Doc/cookbook?

PS: I think biopython is an amazing resource for bioinformatics. Thanks
a lot for making available these resource!

Thanks for your attention!

Best,
Andrea



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