[Biopython-dev] togoWS failure in biopython compilation on MacOSX 10.9.2

[veera singham]

Hi all,

I've recently tried to compile the Biopython 1.63 on MacOsX 10.9.2 
using python version 2.7.5 and a 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 case of TogoWS server error 
or is it caused by the biopython installation itself?

I've seen a similar TogoWS error posted in this group for the Windows.
It seems to be resolved by the TogoWs team, but I'm not so sure on this status. 
Any new update on this?
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