[Biopython-dev] [Bug 2361] Test Suite Failures
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Tue Sep 11 21:00:54 UTC 2007
http://bugzilla.open-bio.org/show_bug.cgi?id=2361
------- Comment #3 from sjf4 at u.washington.edu 2007-09-11 17:00 EST -------
NNGene Test Ouput
= = = = = = = = = = = =
SchemaMatchingTest:Matching schema to strings works correctly.
... ok
Reading and writing motifs to a file ... ok
Reading and writing schemas to a file. ... ok
Reading and writing signatures to a file. ... ok
Retrieve counts for particular patterns in the repository. ... ok
Retrieve all patterns from a repository. ... ok
Retrieve patterns from both sides of the list (top and bottom). ... ok
Retrieve random patterns from the repository. ... ok
Retrieve a certain number of the top patterns. ... ok
Retrieve the top percentge of patterns from the repository. ... ok
Test the ability to remove A rich patterns from the repository. ... ok
Find all motifs in a set of sequences. ... ERROR
Find the difference in motif counts between two sets of sequences. ... ERROR
Convert a sequence into its motif representation. ... ok
Return all unambiguous characters that can be in a motif. ... ok
Find the positions of ambiguous items in a sequence. ... ok
Find all matches in a sequence. ... ok
Make sure motif compiled regular expressions are cached properly. ... ok
Find the number of ambiguous items in a sequence. ... ok
Find how many matches are present in a sequence. ... ok
Convert a string into a representation of motifs. ... ok
Find schemas from sequence inputs. ... ERROR
Find schemas that differentiate between two sets of sequences. ... ERROR
Generating schema from a simple list of motifs. ... ok
Generating schema from a real life set of motifs. ... ERROR
Convert sequences into schema representations. ... ERROR
Find signatures from sequence inputs. ... ERROR
Convert a sequence into its signature representation. ... ok
======================================================================
ERROR: Find all motifs in a set of sequences.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 253, in setUp
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
======================================================================
ERROR: Find the difference in motif counts between two sets of sequences.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 253, in setUp
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
======================================================================
ERROR: Find schemas from sequence inputs.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 416, in setUp
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
======================================================================
ERROR: Find schemas that differentiate between two sets of sequences.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 416, in setUp
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
======================================================================
ERROR: Generating schema from a real life set of motifs.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 546, in t_hard_from_motifs
schema_bank = self._load_schema_repository()
File "test_NNGene.py", line 573, in _load_schema_repository
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
======================================================================
ERROR: Convert sequences into schema representations.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 599, in t_schema_representation
schema_bank = self._load_schema_repository()
File "test_NNGene.py", line 573, in _load_schema_repository
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
======================================================================
ERROR: Find signatures from sequence inputs.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_NNGene.py", line 636, in setUp
seq_record = iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
line 38, in fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
----------------------------------------------------------------------
Ran 28 tests in 0.250s
FAILED (errors=7)
==== ==== ==== ==== ====
SCOP_Astral Test Ouput
= = = = = = = = = = = =
E..E
======================================================================
ERROR: testConstructWithCustomFile (__main__.AstralTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_SCOP_Astral.py", line 55, in testConstructWithCustomFile
assert astral.getSeqBySid('d3sdha_').data == "AAAAA"
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/SCOP/__init__.py",
line 806, in getSeqBySid
return self.fasta_dict[domain].seq
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 214, in __getitem__
return dict.__getitem__(self,key)
KeyError: 'd3sdha_'
======================================================================
ERROR: testGetSeq (__main__.AstralTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_SCOP_Astral.py", line 43, in testGetSeq
assert self.astral.getSeqBySid('d3sdha_').data == "AAAAA"
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/SCOP/__init__.py",
line 806, in getSeqBySid
return self.fasta_dict[domain].seq
File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__init__.py",
line 214, in __getitem__
return dict.__getitem__(self,key)
KeyError: 'd3sdha_'
----------------------------------------------------------------------
Ran 4 tests in 0.114s
FAILED (errors=2)
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