[Biopython-dev] TogoWS test failure, was: Compiling Biopython on 64 bit Windows

[Peter Cock]

On Fri, May 16, 2014 at 9:13 AM, veera singham <vee_rs at yahoo.com> wrote:
> Peter Cock <p.j.a.cock <at> googlemail.com> writes:
>
>>
>>OnSat,Apr 19, 2014 at 1:23PM,PeterCock<p.j.a.cock <at>googlemail.com> wrote:
>> The TogoWS team confirmed this is a problem with the
>> server and expect it to be fixed shortly.
>>
>> Peter
>>
>> For the record, this is working now :)
>>
>> Peter
>>
>
>
> Hi all,
>
> I've recently tried to compile the Biopython 1.63 on MacOsX 10.9.2
> using python version 2.7.5 and had similar TogoWS test failure.
>
> Here I've attached the log files of the error command:
>
> ERROR: test_genebank_to_embl (test_TogoWS.TogoConvert)
> Conversion of GenBank to EMBL.
>
> Traceback (most recent call last):
> File"test_TogoWS.py", line 508, in test_genbank_to_embl
> new = SeqIO.read(TogoWS.convert(handle, "genbank", "embl"),"embl")
> File "Users/veerasingham/Downloads/
> biopython-1.63/build/lib.macosx-10.9-intel2.7
> /Bio/SEqIO/_init_.py:,line 650, in read
> raise ValueError("No records found in handle")
> ValueError:No records found in handle
>
> ERROR:test_genbank_to_fasta (test_TogoWS.TogoConvert)
> Conversion of GenBank to FASTA.
>
> Traceback (most recent call last):
> File"test_TogoWS.py", line 508, in test_genbank_to_fasta
> new = SeqIO.read(TogoWS.convert(handle, "genbank", "fasta"),"fasta")
> File "Users/veerasingham/Downloads/
> biopython-1.63/build/lib.macosx-10.9-intel2.7
> /Bio/SEqIO/_init_.py:,line 650, in read
> raise ValueError("No records found in handle")
> ValueError:No records found in handle
>
> All the other test is OK.
>
> The Biopython, however is successfully installed and seemed to work according to
> simple test code as suggested over the installation web page.
>
> I wonder if this error is due to a similar case due to the TogoWS server error?
> Can anyone suggest how to fixed  this?
>
> I afraid that this error may affect my subsequent analysis involving biopython.
>
> Please let me know if there is any update on this.
>
> Thanks.
>
> Cheers,
>
> Veera

Hi Veera,

My apologies for the delayed reply - Google thought your email was spam :(

If TogoWS always fails for you (retesting a few days later), but not
for other people, then perhaps there is a problem with your network?
For example, sometimes proxy settings can cause problems...

It is more likely that this was a temporary problem - either with the
network or with the TogoWS server. Like any online service, from
time to time it can be unavailable, and so our tests using it will fail.

If you are not using TogoWS this is nothing to worry about. Similarly,
this also happens with the NCBI Entrez and BLAST services as well
sometimes.

Regards,

Peter