[BioPython] Interacting with GenBank

[Jan T. Kim]

On Sat, Mar 26, 2005 at 10:50:30AM -0600, Kari Linder wrote:
> Here is the script I am working with :
> 
> from Bio.WWW import NCBI
> 
> 
> search_command = 'Search'
> search_database = 'Nucleotide'
> return_format = 'Fasta'
> search_term = 'Ciliphora'
> 
> 
> 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()
> 
> It is basically from section  "2.5 Connecting with biological 
> databases" in the biopython tutorial, and it works being that it gives 
> me an html file, however when I open the file it says that the results 
> cannot be displayed. Has anyone had this problem?

Not me...

Can you be more specific about which is "it" which "says that the results
cannot be displayed"? If "it" is your operating system, then there's
little that Biopython or Genbank can do about that, if, however, "it"
is a Biopython routine, then perhaps some HTML has changed such that
the parser cannot understand it anymore or something like that. Please
provide a transcript of the error.

Best regards (and happy Easter), Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: jtk at cmp.uea.ac.uk                               |
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