[Biopython] ERROR: test_doctests
Michal
mictadlo at gmail.com
Sat Apr 9 02:39:08 EDT 2011
$ python test_Tutorial.py
Runing Tutorial doctests...
**********************************************************************
File "test_Tutorial.py", line 98, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02697
Failed example:
orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.gbk", "genbank"))
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02697[3]>", line
1, in <module>
orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.gbk",
"genbank"))
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 670, in to_dict
for record in sequences:
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 499, in parse
handle = open(handle, "rU")
IOError: [Errno 2] No such file or directory: 'ls_orchid.gbk'
**********************************************************************
File "test_Tutorial.py", line 99, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02697
Failed example:
len(orchid_dict)
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02697[4]>", line
1, in <module>
len(orchid_dict)
NameError: name 'orchid_dict' is not defined
**********************************************************************
File "test_Tutorial.py", line 101, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02697
Failed example:
seq_record = orchid_dict["Z78475.1"]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02697[5]>", line
1, in <module>
seq_record = orchid_dict["Z78475.1"]
NameError: name 'orchid_dict' is not defined
**********************************************************************
File "test_Tutorial.py", line 102, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02697
Failed example:
print seq_record.description
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02697[6]>", line
1, in <module>
print seq_record.description
NameError: name 'seq_record' is not defined
**********************************************************************
File "test_Tutorial.py", line 104, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02697
Failed example:
print repr(seq_record.seq)
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02697[7]>", line
1, in <module>
print repr(seq_record.seq)
NameError: name 'seq_record' is not defined
**********************************************************************
File "test_Tutorial.py", line 99, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02816
Failed example:
seguid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.gbk", "genbank"),
lambda rec : seguid(rec.seq))
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02816[4]>", line
2, in <module>
lambda rec : seguid(rec.seq))
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 670, in to_dict
for record in sequences:
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 499, in parse
handle = open(handle, "rU")
IOError: [Errno 2] No such file or directory: 'ls_orchid.gbk'
**********************************************************************
File "test_Tutorial.py", line 101, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02816
Failed example:
record = seguid_dict["MN/s0q9zDoCVEEc+k/IFwCNF2pY"]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02816[5]>", line
1, in <module>
record = seguid_dict["MN/s0q9zDoCVEEc+k/IFwCNF2pY"]
NameError: name 'seguid_dict' is not defined
**********************************************************************
File "test_Tutorial.py", line 102, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02816
Failed example:
print record.id
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02816[6]>", line
1, in <module>
print record.id
NameError: name 'record' is not defined
**********************************************************************
File "test_Tutorial.py", line 104, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02816
Failed example:
print record.description
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02816[7]>", line
1, in <module>
print record.description
NameError: name 'record' is not defined
**********************************************************************
File "test_Tutorial.py", line 98, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02849
Failed example:
orchid_dict = SeqIO.index("ls_orchid.gbk", "genbank")
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02849[3]>", line
1, in <module>
orchid_dict = SeqIO.index("ls_orchid.gbk", "genbank")
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 787, in index
return _index._IndexedSeqFileDict(filename, format, alphabet,
key_function)
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/_index.py",
line 78, in __init__
random_access_proxy = proxy_class(filename, format, alphabet)
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/_index.py",
line 615, in __init__
SeqFileRandomAccess.__init__(self, filename, format, alphabet)
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/SeqIO/_index.py",
line 487, in __init__
self._handle = open(filename, "rb")
IOError: [Errno 2] No such file or directory: 'ls_orchid.gbk'
**********************************************************************
File "test_Tutorial.py", line 99, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02849
Failed example:
len(orchid_dict)
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02849[4]>", line
1, in <module>
len(orchid_dict)
NameError: name 'orchid_dict' is not defined
**********************************************************************
File "test_Tutorial.py", line 101, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02849
Failed example:
seq_record = orchid_dict["Z78475.1"]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02849[5]>", line
1, in <module>
seq_record = orchid_dict["Z78475.1"]
NameError: name 'orchid_dict' is not defined
**********************************************************************
File "test_Tutorial.py", line 102, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02849
Failed example:
print seq_record.description
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02849[6]>", line
1, in <module>
print seq_record.description
NameError: name 'seq_record' is not defined
**********************************************************************
File "test_Tutorial.py", line 104, in
__main__.TutorialDocTestHolder.doctest_test_from_line_02849
Failed example:
seq_record.seq
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_02849[7]>", line
1, in <module>
seq_record.seq
NameError: name 'seq_record' is not defined
**********************************************************************
File "test_Tutorial.py", line 98, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03390
Failed example:
alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03390[3]>", line
1, in <module>
alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/AlignIO/__init__.py",
line 427, in read
first = iterator.next()
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/AlignIO/__init__.py",
line 333, in parse
handle = open(handle, "rU")
IOError: [Errno 2] No such file or directory: 'PF05371_seed.sth'
**********************************************************************
File "test_Tutorial.py", line 99, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03390
Failed example:
print alignment
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03390[4]>", line
1, in <module>
print alignment
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 98, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03413
Failed example:
alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03413[3]>", line
1, in <module>
alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/AlignIO/__init__.py",
line 427, in read
first = iterator.next()
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/AlignIO/__init__.py",
line 333, in parse
handle = open(handle, "rU")
IOError: [Errno 2] No such file or directory: 'PF05371_seed.sth'
**********************************************************************
File "test_Tutorial.py", line 99, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03413
Failed example:
print "Alignment length %i" % alignment.get_alignment_length()
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03413[4]>", line
1, in <module>
print "Alignment length %i" % alignment.get_alignment_length()
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 101, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03413
Failed example:
for record in alignment:
print "%s - %s" % (record.seq, record.id)
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03413[5]>", line
1, in <module>
for record in alignment:
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 110, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03413
Failed example:
for record in alignment:
if record.dbxrefs:
print record.id, record.dbxrefs
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03413[6]>", line
1, in <module>
for record in alignment:
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 98, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[3]>", line
1, in <module>
alignment = AlignIO.read("PF05371_seed.sth", "stockholm")
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/AlignIO/__init__.py",
line 427, in read
first = iterator.next()
File
"/home/mictadlo/apps/pymodules/lib64/python2.7/site-packages/Bio/AlignIO/__init__.py",
line 333, in parse
handle = open(handle, "rU")
IOError: [Errno 2] No such file or directory: 'PF05371_seed.sth'
**********************************************************************
File "test_Tutorial.py", line 99, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print "Number of rows: %i" % len(alignment)
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[4]>", line
1, in <module>
print "Number of rows: %i" % len(alignment)
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 101, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
for record in alignment:
print "%s - %s" % (record.seq, record.id)
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[5]>", line
1, in <module>
for record in alignment:
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 110, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[6]>", line
1, in <module>
print alignment
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 119, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[3:7]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[7]>", line
1, in <module>
print alignment[3:7]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 125, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[2,6]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[8]>", line
1, in <module>
print alignment[2,6]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 127, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[2].seq[6]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[9]>", line
1, in <module>
print alignment[2].seq[6]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 129, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[:,6]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[10]>", line
1, in <module>
print alignment[:,6]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 131, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[3:6,:6]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[11]>", line
1, in <module>
print alignment[3:6,:6]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 136, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[:,:6]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[12]>", line
1, in <module>
print alignment[:,:6]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 145, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[:,6:9]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[13]>", line
1, in <module>
print alignment[:,6:9]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 154, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print alignment[:,9:]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[14]>", line
1, in <module>
print alignment[:,9:]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 163, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
edited = alignment[:,:6] + alignment[:,9:]
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[15]>", line
1, in <module>
edited = alignment[:,:6] + alignment[:,9:]
NameError: name 'alignment' is not defined
**********************************************************************
File "test_Tutorial.py", line 164, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print edited
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[16]>", line
1, in <module>
print edited
NameError: name 'edited' is not defined
**********************************************************************
File "test_Tutorial.py", line 173, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
edited.sort()
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[17]>", line
1, in <module>
edited.sort()
NameError: name 'edited' is not defined
**********************************************************************
File "test_Tutorial.py", line 174, in
__main__.TutorialDocTestHolder.doctest_test_from_line_03920
Failed example:
print edited
Exception raised:
Traceback (most recent call last):
File "/usr/lib64/python2.7/doctest.py", line 1248, in __run
compileflags, 1) in test.globs
File "<doctest
__main__.TutorialDocTestHolder.doctest_test_from_line_03920[18]>", line
1, in <module>
print edited
NameError: name 'edited' is not defined
**********************************************************************
6 items had failures:
5 of 8 in __main__.TutorialDocTestHolder.doctest_test_from_line_02697
4 of 8 in __main__.TutorialDocTestHolder.doctest_test_from_line_02816
5 of 8 in __main__.TutorialDocTestHolder.doctest_test_from_line_02849
2 of 5 in __main__.TutorialDocTestHolder.doctest_test_from_line_03390
4 of 7 in __main__.TutorialDocTestHolder.doctest_test_from_line_03413
16 of 19 in __main__.TutorialDocTestHolder.doctest_test_from_line_03920
***Test Failed*** 36 failures.
Traceback (most recent call last):
File "test_Tutorial.py", line 129, in <module>
raise RuntimeError("%i/%i tests failed" % tests)
RuntimeError: 36/448 tests failed
On 04/07/2011 11:43 PM, Peter Cock wrote:
> On Thu, Apr 7, 2011 at 2:21 PM, Michal<mictadlo at gmail.com> wrote:
>> Hello,
>> During test BioPython 1.57 on Fedora 14(64bit) has given me the following
>> error:
>> $ python setup.py build
>> $ python setup.py test
>> .....
>> Bio.PDB.Polypeptide docstring test ... ok
>> ======================================================================
>> ERROR: test_doctests (test_Tutorial.TutorialTestCase)
>> Run tutorial doctests.
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "test_Tutorial.py", line 115, in test_doctests
>> ValueError: 6 Tutorial doctests failed: test_from_line_02697,
>> test_from_line_02816, test_from_line_02849, test_from_line_03390,
>> test_from_line_03413, test_from_line_03920
>>
>> ----------------------------------------------------------------------
>> Ran 150 tests in 260.287 seconds
>>
>> FAILED (failures = 1)
>>
>> Michal
> Hmm. Can you try this, it should give some more detailed output:
>
> $ cd Tests/
> $ python test_Tutorial.py
> Runing Tutorial doctests...
> Tests done
>
> (although we're expecting it to fail on your machine).
>
> Thanks,
>
> Peter
>
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