[Biopython-dev] Re: [BioPython] Patch to fix testing failures in biopython-1.30

[Michiel Jan Laurens de Hoon]

I tried these urls today and it seems that both emblfetch and dbfetch 
work. Were there any problems using the emblfetch urls?

--Michiel.

Bill Barnard wrote:
> The fixed problem is in Bio/dbdefs/pdb.py - the location of the cgi has
> changed, and there appears to be an extraneous newline in the returned
> text.
> 
>  pdb_ebi_cgi = CGIDB(
>      name="pdb-ebi-cgi",
> -    cgi="http://www.ebi.ac.uk/cgi-bin/emblfetch",
> -    url="http://www.ebi.ac.uk/cgi-bin/emblfetch",
> +    cgi="http://www.ebi.ac.uk/cgi-bin/dbfetch",
> +    url="http://www.ebi.ac.uk/cgi-bin/dbfetch",
>      delay=5.0,
>      params=[("db", "PDB"),
>              ("format", "default"),   # also Fasta, bsml, agave available
>              ("style", "raw"),
>              ],
>      key="id",
> -    failure_cases=[(not_header_expr, "results do not look like PDB format")]
> +    failure_cases=[(not_header_expr, "pdb_ebi_cgi results do not look like PDB format")]
>      )
>