[Biopython] ERROR: Bio.Entrez.efetch(genome, X52960, ...) and ERROR: Bio.ExPASy.get_sprot_raw("O23729")

[ming.xue at boehringer-ingelheim.com]

Hi All,

I was installing biopython 1.55 over python 2.6 and testing generated the
error:
======================================================================
ERROR: Bio.Entrez.efetch(genome, X52960, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_SeqIO_online.py", line 85, in <lambda>
    method = lambda x : x.simple(d, f, e, l, c)
  File "test_SeqIO_online.py", line 63, in simple
    record = SeqIO.read(handle, f)
  File
"/src/biopython-1.55/build/lib.linux-x86_64-2.6/Bio/SeqIO/__init__.py", line
585, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

======================================================================
ERROR: Bio.ExPASy.get_sprot_raw("O23729")
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_SeqIO_online.py", line 53, in test_get_sprot_raw
    "internet (or maybe just ExPASy) not available")
MissingExternalDependencyError: internet (or maybe just ExPASy) not available

----------------------------------------------------------------------
Ran 144 tests in 93.664 seconds

FAILED (failures = 1)

Since I am behind proxy with ntlm authentication, my guess the issue is
related to firewall. I tried some solution from internet such as ntlm-map and
python-ntlm but no luck. Any suggestions?

Best and thanks,

MX