[Biopython] Biopython error

[Peter Cock]

If anyone has any bright ideas, Damian filed this on GitHub, so please
comment there:

https://github.com/biopython/biopython/issues/915

Peter

On Mon, Aug 22, 2016 at 10:07 PM, Damian Menning <dmenning at mail.usf.edu> wrote:
> Hello everyone,
>
>   I am running a Python 2.7 script that has worked in the past but now is
> throwing an error.  I am wondering if there has been a change recently that
> may be causing the problem.
>
>   My script searches NCBI using each Genus species name for a list
> (species), a general category like bony fish (cat), and a search term like
> 16S (add_term) and returns a list of non-replicated ids.  The script is
> below:
>
> def ncbi_search(species_list):
>     global full_gi_list
>     print "\nSearching NCBI for"+str(species)+' and '+str(add_term)+' and
> '+str(cat)+'\n'
>     search_handle=Entrez.esearch(db="nucleotide", term=cat + ' AND ' +
> add_term + ' AND ' + species, usehistory="y", RetMax=9999)
>     search_results=Entrez.read(search_handle)
>     search_handle.close()
>     gi_list=search_results["IdList"]
>     full_gi_list.extend(gi_list)
>     return full_gi_list
>
>     for species in species_list:
>         ncbi_search(species_list)
>
> The error I am getting is:
>
> Traceback (most recent call last):
>   File "D:\Python27\0
> eDNA\02_GenBank_get_fasta_or_gb_no_repeats_1_search_criter
> ia.py", line 98, in <module>
>     ncbi_search(species_list)
>   File "D:\Python27\0
> eDNA\02_GenBank_get_fasta_or_gb_no_repeats_1_search_criter
> ia.py", line 49, in ncbi_search
>     search_results = Entrez.read(search_handle)
>   File "C:\Python27\lib\site-packages\Bio\Entrez\__init__.py", line 376, in
> read
>
>     record = handler.read(handle)
>   File "C:\Python27\lib\site-packages\Bio\Entrez\Parser.py", line 205, in
> read
>     self.parser.ParseFile(handle)
>   File "C:\Python27\lib\site-packages\Bio\Entrez\Parser.py", line 343, in
> endEle
> mentHandler
>     raise RuntimeError(value)
> RuntimeError: Invalid db name specified: nuccore
>
>   Any ideas on what is going wrong?
>
>   Thanks for the help
>
>   Damian
>
> --
> Damian Menning, Ph.D.
>
> "There are two types of academics. Those who use the Oxford comma, those who
> don't and those who should."
>
> Standard comma - You know Bob, Sue and Greg? They came to my house.
> Oxford comma - You know Bob, Sue, and Greg? They came to my house.
> Walken Comma - You know, Bob, Sue, and Greg? They came, to my house.
> Shatner comma - You, know, Bob, Sue, and Greg? They, came, to my house.
>
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