Entering edit mode
11.4 years ago
l0o0
▴
220
I downloaded the tar file from the biopython website, extracted and intalled it as the readme told.
python setup.py build
python setup.py test
when i did the second command, there came some errors, the errors are above:
======================================================================
FAIL: Test an input file containing a single sequence.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_Clustalw_tool.py", line 166, in test_single_sequence
self.assertTrue(str(err) == "No records found in handle")
AssertionError
======================================================================
ERROR: Test Entrez.read from URL
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_Entrez_online.py", line 34, in test_read_from_url
rec = Entrez.read(einfo)
File "/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/__init__.py", line 362, in read
record = handler.read(handle)
File "/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/Parser.py", line 184, in read
self.parser.ParseFile(handle)
File "/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/Parser.py", line 322, in endElementHandler
raise RuntimeError(value)
RuntimeError: Unable to open connection to #DbInfo?dbaf=
======================================================================
ERROR: Run tutorial doctests.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_Tutorial.py", line 152, in test_doctests
ValueError: 4 Tutorial doctests failed: test_from_line_05671, test_from_line_06030, test_from_line_06190, test_from_line_06479
----------------------------------------------------------------------
Ran 213 tests in 1621.002 seconds
FAILED (failures = 3)
How can i solve these errors?
are you using python>=3?
i have python 3 installed in my machine, but i also have python 2.65 installed. python = python 2.6.5 by default.
You may well get help here, but it's probably also a good idea to send a message to the Biopython mailing list with details of your setup (OS/Python version and version of Clustal you have installed in your $PATH) along with this information. List details are here: http://biopython.org/wiki/Mailing_lists.
Thanks for your advice. I will try this way.