[Biopython-dev] [Bug 2468] New: Tutorial needs a fix: Bio.WWW.NCBI

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2468

           Summary: Tutorial needs a fix: Bio.WWW.NCBI
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Documentation
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


I am trying to follow the recipe at
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc14 which contains the
following split into several chunks (I don't like this style personally, but
that's not the issue here):

#! /usr/bin/python
from Bio.WWW import NCBI

search_command = 'Search'
search_database = 'Taxonomy'
return_format = 'FASTA'
search_term = 'Cypripedioideae'

my_browser = 'lynx'

result_handle = NCBI.query(search_command, search_database, term = search_term,
doptcmdl = return_format)

import os
result_file_name = os.path.join(os.getcwd(), "results.html")
result_file = open(result_file_name, "w")
result_file.write(result_handle.read())
result_file.close()

if my_browser == "lynx":
    os.system("lynx -force_html " + result_file_name)
elif my_browser == "netscape":
    os.system("netscape file:" + result_file_name)


I end up with a lynx browser opened with the Entrez search page pre-filled with
the 'Cypripedioideae' as the query string. Unfortunately, I have to click on
the 
condensed results to get the taxonomy listing under the word 'Cypripedioideae'.
The line I am talking about is close the the end of the output:

   [ ] 1: Cypripedioideae, subfamily, monocots Links



BTW, other the links from the page do not work because they point to
http://localhost/....




/usr/lib/python2.5/site-packages/Bio/WWW/NCBI.py:34: DeprecationWarning:
Bio.WWW.NCBI is deprecated. The functions in Bio.WWW.NCBI are now available
from Bio.Entrez.
  DeprecationWarning)

The section needs updating. I am somewhat surprised I cannot access NCBI
Taxonomy easily. Priobably will have to browse the source code and forget
Tutorail and Cookbook. ;)


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