biopython 1.54 のテストを動かしてみた
コマンドがみつからないとかあるのかぁ
実効結果
Ran 144 tests in 254.850 seconds
FAILED (failures = 10)
tar zxvf biopython-1.54.tar.gz
cd biopython-1.54
python setup.py build
python setup.py test
running test
test_Ace ... ok
test_AlignIO ... ok
test_AlignIO_convert ... ok
test_BioSQL ... /home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/BioSQL/Loader.py:797: UserWarning: order location operators are not fully supported
% feature.location_operator)
ok
test_BioSQL_SeqIO ... /home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/BioSQL/Loader.py:797: UserWarning: bond location operators are not fully supported
% feature.location_operator)
ok
test_CAPS ... ok
test_Clustalw ... ok
test_Clustalw_tool ... ERROR
test_Cluster ... ok
test_CodonTable ... ok
test_CodonUsage ... ok
test_Compass ... ok
test_Crystal ... ok
test_Dialign_tool ... skipping. Environment variable DIALIGN2_DIR for DIALIGN2-2 missing.
test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
test_Emboss ... ERROR
test_EmbossPhylipNew ... FAIL
test_EmbossPrimer ... ok
test_Entrez ... ok
test_Enzyme ... ok
test_FSSP ... ok
test_Fasta ... ok
test_File ... ok
test_GACrossover ... ok
test_GAMutation ... ok
test_GAOrganism ... ok
test_GAQueens ... ok
test_GARepair ... ok
test_GASelection ... ok
test_GFF ... skipping. Environment is not configured for this test (not important if you do not plan to use Bio.GFF).
test_GFF2 ... skipping. Install MySQLdb if you want to use Bio.GFF.
test_GenBank ... ok
test_GenomeDiagram ... skipping. Install reportlab if you want to use Bio.Graphics.
test_GraphicsBitmaps ... skipping. Install ReportLab if you want to use Bio.Graphics.
test_GraphicsChromosome ... skipping. Install reportlab if you want to use Bio.Graphics.
test_GraphicsDistribution ... skipping. Install reportlab if you want to use Bio.Graphics.
test_GraphicsGeneral ... skipping. Install reportlab if you want to use Bio.Graphics.
test_HMMCasino ... ok
test_HMMGeneral ... ok
test_HotRand ... ok
test_IsoelectricPoint ... ok
test_KDTree ... ok
test_KEGG ... ok
test_KeyWList ... ok
test_Location ... ok
test_LocationParser ... ok
test_LogisticRegression ... ok
test_MEME ... ok
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
test_MarkovModel ... ok
test_Medline ... ok
test_Motif ... ok
test_Muscle_tool ... FAIL
test_NCBIStandalone ... ok
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
test_NCBI_qblast ... ERROR
test_NNExclusiveOr ... ok
test_NNGene ... ok
test_NNGeneral ... ok
test_Nexus ... ok
test_PDB ... ok
test_ParserSupport ... ok
test_Pathway ... ok
test_Phd ... ok
test_Phylo ... ok
test_PhyloXML ... ok
test_Phylo_depend ... skipping. Install NetworkX if you want to use Bio.Phylo._utils.
test_PopGen_FDist ... skipping. Install FDist if you want to use Bio.PopGen.FDist.
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
test_PopGen_GenePop_nodepend ... ok
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use Bio.PopGen.SimCoal.
test_PopGen_SimCoal_nodepend ... ok
test_Prank_tool ... FAIL
test_Probcons_tool ... FAIL
test_ProtParam ... ok
test_Restriction ... ok
test_SCOP_Astral ... ok
test_SCOP_Cla ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SVDSuperimposer ... ok
test_SeqIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_convert ... ok
test_SeqIO_features ... ok
test_SeqIO_index ... ok
test_SeqIO_online ... ok
test_SeqRecord ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SubsMat ... ok
test_SwissProt ... ok
test_TCoffee_tool ... FAIL
test_UniGene ... ok
test_UniGene_obsolete ... ok
test_Wise ... INFO trying again with the linear model
FAIL
test_align ... ok
test_geo ... ok
test_interpro ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite1 ... ok
test_prosite2 ... ok
test_prosite_patterns ... ok
test_psw ... ok
test_seq ... ok
test_translate ... ok
test_trie ... ok
test_triefind ... ok
Bio.Application docstring test ... ok
Bio.Seq docstring test ... ok
Bio.SeqFeature docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.SffIO docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.Align docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Blast.Applications docstring test ... ok
Bio.Clustalw docstring test ... ok
Bio.Emboss.Applications docstring test ... ok
Bio.KEGG.Compound docstring test ... ok
Bio.KEGG.Enzyme docstring test ... ok
Bio.Wise docstring test ... FAIL
Bio.Wise.psw docstring test ... ok
Bio.Motif docstring test ... ok
Bio.Statistics.lowess docstring test ... ok
======================================================================
ERROR: test_Clustalw_tool
- -
Traceback (most recent call last):
File "run_tests.py", line 267, in runTest
suite = unittest.TestLoader().loadTestsFromName(name)
File "/usr/lib/python2.5/unittest.py", line 533, in loadTestsFromName
module = __import__('.'.join(parts_copy))
File "test_Clustalw_tool.py", line 104, in
assert "has only one sequence present" in str(err)
AssertionError
======================================================================
ERROR: test_Emboss
- -
Traceback (most recent call last):
File "run_tests.py", line 267, in runTest
suite = unittest.TestLoader().loadTestsFromName(name)
File "/usr/lib/python2.5/unittest.py", line 533, in loadTestsFromName
module = __import__('.'.join(parts_copy))
File "test_Emboss.py", line 78, in
if get_emboss_version() < (6,1,0):
File "test_Emboss.py", line 75, in get_emboss_version
raise ValueError(stdout)
ValueError: /bin/sh: embossversion: コマンドが見つかりません======================================================================
ERROR: pseudosample a phylip DNA alignment written with AlignIO
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 267, in test_bootstrap_AlignIO_DNA
self.check_bootstrap("Phylip/opuntia.phy", "phylip")
File "test_EmbossPhylipNew.py", line 249, in check_bootstrap
% (return_code, str(cline)))
ValueError: Return code 127 from:
fseqboot -auto -filter -outfile=test_file -sequence=Phylip/opuntia.phy -seqtype=d -reps=2======================================================================
ERROR: pseudosample a phylip protein alignment written with AlignIO
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 276, in test_bootstrap_AlignIO_protein
self.check_bootstrap("Phylip/hedgehog.phy", "phylip", "p")
File "test_EmbossPhylipNew.py", line 249, in check_bootstrap
% (return_code, str(cline)))
ValueError: Return code 127 from:
fseqboot -auto -filter -outfile=test_file -sequence=Phylip/hedgehog.phy -seqtype=p -reps=2======================================================================
ERROR: pseudosample a phylip DNA alignment
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 262, in test_bootstrap_phylip_DNA
self.check_bootstrap("Phylip/horses.phy", "phylip")
File "test_EmbossPhylipNew.py", line 249, in check_bootstrap
% (return_code, str(cline)))
ValueError: Return code 127 from:
fseqboot -auto -filter -outfile=test_file -sequence=Phylip/horses.phy -seqtype=d -reps=2======================================================================
ERROR: pseudosample a phylip protein alignment
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 271, in test_bootstrap_phylip_protein
self.check_bootstrap("Phylip/interlaced.phy", "phylip", "p")
File "test_EmbossPhylipNew.py", line 249, in check_bootstrap
% (return_code, str(cline)))
ValueError: Return code 127 from:
fseqboot -auto -filter -outfile=test_file -sequence=Phylip/interlaced.phy -seqtype=p -reps=2======================================================================
ERROR: Calculate a distance matrix from an alignment written by AlignIO
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 140, in test_distances_from_AlignIO_DNA
self.distances_from_alignment("Phylip/opuntia.phy")
File "test_EmbossPhylipNew.py", line 115, in distances_from_alignment
% (return_code, str(cline)))
ValueError: Return code 127 from:
fdnadist -auto -outfile=test_file -sequence=Phylip/opuntia.phy -method=j======================================================================
ERROR: Calculate a distance matrix from an phylip alignment
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 135, in test_distances_from_phylip_DNA
self.distances_from_alignment("Phylip/horses.phy")
File "test_EmbossPhylipNew.py", line 115, in distances_from_alignment
% (return_code, str(cline)))
ValueError: Return code 127 from:
fdnadist -auto -outfile=test_file -sequence=Phylip/horses.phy -method=j======================================================================
ERROR: Calculate distance matrix from an AlignIO written protein alignment
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 154, in test_distances_from_protein_AlignIO
self.distances_from_alignment("Phylip/hedgehog.phy", DNA=False)
File "test_EmbossPhylipNew.py", line 115, in distances_from_alignment
% (return_code, str(cline)))
ValueError: Return code 127 from:
fprotdist -auto -outfile=test_file -sequence=Phylip/hedgehog.phy -method=j======================================================================
ERROR: Calculate a distance matrix from phylip protein alignment
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 149, in test_distances_from_protein_phylip
self.distances_from_alignment("Phylip/interlaced.phy", DNA=False)
File "test_EmbossPhylipNew.py", line 115, in distances_from_alignment
% (return_code, str(cline)))
ValueError: Return code 127 from:
fprotdist -auto -outfile=test_file -sequence=Phylip/interlaced.phy -method=j======================================================================
ERROR: Make a parsimony tree from protein alignment written with AlignIO
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 221, in test_parsimony_from_AlignIO_protein
self.parsimony_tree("Phylip/interlaced.phy", "phylip", DNA=False)
File "test_EmbossPhylipNew.py", line 192, in parsimony_tree
% (return_code, str(cline)))
ValueError: Return code 127 from:
fprotpars -auto -stdout -sequence=Phylip/interlaced.phy -outtreefile=test_file======================================================================
ERROR: Make a parsimony tree from an alignment written with AlignIO
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 207, in test_parsimony_tree_from_AlignIO_DNA
self.parsimony_tree("Phylip/opuntia.phy", "phylip")
File "test_EmbossPhylipNew.py", line 192, in parsimony_tree
% (return_code, str(cline)))
ValueError: Return code 127 from:
fdnapars -auto -stdout -sequence=Phylip/opuntia.phy -outtreefile=test_file======================================================================
ERROR: Calculate a consensus tree with fconsense
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 293, in test_fconsense
% (return_code, str(cline)))
ValueError: Return code 127 from:
fconsense -auto -filter -intreefile=Phylip/horses.tree -outtreefile=test_file======================================================================
ERROR: Calculate the distance between trees with ftreedist
- -
Traceback (most recent call last):
File "test_EmbossPhylipNew.py", line 308, in test_ftreedist
% (return_code, str(cline)))
ValueError: Return code 127 from:
ftreedist -auto -filter -outfile=test_file -intreefile=Phylip/horses.tree======================================================================
ERROR: Simple muscle call using long file
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 272, in test_long
align = AlignIO.read(child.stdout, "clustal")
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/AlignIO/__init__.py", line 423, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle======================================================================
ERROR: Simple muscle call using Clustal output with a MUSCLE header
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 202, in test_simple_clustal
align = AlignIO.read(child.stdout, "clustal")
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/AlignIO/__init__.py", line 423, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle======================================================================
ERROR: Simple muscle call using strict Clustal output
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 232, in test_simple_clustal_strict
align = AlignIO.read(child.stdout, "clustal")
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/AlignIO/__init__.py", line 423, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle======================================================================
ERROR: Simple alignment using stdin
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 301, in test_using_stdin
align = AlignIO.read(child.stdout, "clustal")
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/AlignIO/__init__.py", line 423, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle======================================================================
ERROR: Simple muscle call with multiple output formats
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 330, in test_with_multiple_output_formats
align = AlignIO.read(child.stdout, "clustal")
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/AlignIO/__init__.py", line 423, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle======================================================================
FAIL: Simple round-trip through app doing a profile alignment
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 132, in test_Muscle_profile_simple
self.assertEqual(child.returncode, 0)
AssertionError: 127 != 0======================================================================
FAIL: Simple round-trip through app just infile and outfile
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 88, in test_Muscle_simple
self.assertEqual(child.returncode, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app with a switch and valued option
- -
Traceback (most recent call last):
File "test_Muscle_tool.py", line 111, in test_Muscle_with_options
self.assertEqual(child.returncode, 0)
AssertionError: 127 != 0======================================================================
ERROR: test_NCBI_qblast
- -
Traceback (most recent call last):
File "run_tests.py", line 267, in runTest
suite = unittest.TestLoader().loadTestsFromName(name)
File "/usr/lib/python2.5/unittest.py", line 533, in loadTestsFromName
module = __import__('.'.join(parts_copy))
File "test_NCBI_qblast.py", line 98, in
assert found_result, "Missing %s in alignments" % expected_hit
AssertionError: Missing 18409071 in alignments
======================================================================
FAIL: Round-trip with complex command line.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 144, in test_Prank_complex_command_line
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Simple round-trip through app with infile.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 85, in test_Prank_simple
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Simple round-trip through app with infile, output in NEXUS
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 109, in test_Prank_simple_with_NEXUS_output
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Convert FASTA to FASTA format.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 213, in test_convert_to_fasta
self.conversion(8, "fas", "fasta")
File "test_Prank_tool.py", line 174, in conversion
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Convert FASTA to Inteligenetics format.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 195, in test_convert_to_ig
self.conversion(1, "igs", "ig")
File "test_Prank_tool.py", line 174, in conversion
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Convert FASTA to NBRF/PIR format.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 204, in test_convert_to_nbrf
self.conversion(3, "nbr", "pir")
File "test_Prank_tool.py", line 174, in conversion
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Convert FASTA to PHYLIP format.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 221, in test_convert_to_phylip
self.conversion(12, "phy", "phylip")
File "test_Prank_tool.py", line 174, in conversion
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Convert FASTA to PHYLIP 3.2 format.
- -
Traceback (most recent call last):
File "test_Prank_tool.py", line 217, in test_convert_to_phylip32
self.conversion(11, "phy", "phylip")
File "test_Prank_tool.py", line 174, in conversion
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app and read clustalw alignment from stdout
- -
Traceback (most recent call last):
File "test_Probcons_tool.py", line 72, in test_Probcons_alignment_clustalw
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app and read fasta alignment from stdout
- -
Traceback (most recent call last):
File "test_Probcons_tool.py", line 49, in test_Probcons_alignment_fasta
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app with complex command line and output file
- -
Traceback (most recent call last):
File "test_Probcons_tool.py", line 100, in test_Probcons_complex_commandline
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app and read clustal alignment from file
- -
Traceback (most recent call last):
File "test_TCoffee_tool.py", line 59, in test_TCoffee_1
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app and read pir alignment from file
- -
Traceback (most recent call last):
File "test_TCoffee_tool.py", line 83, in test_TCoffee_2
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
FAIL: Round-trip through app and read clustalw alignment from file
- -
Traceback (most recent call last):
File "test_TCoffee_tool.py", line 111, in test_TCoffee_3
self.assertEqual(return_code, 0)
AssertionError: 127 != 0======================================================================
ERROR: Call dnal with optional arguments, and do a trivial check on the output.
- -
Traceback (most recent call last):
File "test_Wise.py", line 39, in test_align
temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 98, in align
return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 100, in align
raise OSError("%s returned %s" % (" ".join(cmdline), status))
OSError: dnal returned 127======================================================================
FAIL: Call dnal, and do a trivial check on its output.
- -
Traceback (most recent call last):
File "test_Wise.py", line 26, in test_dnal
self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000 seq1.fna seq2.fna"))
AssertionError======================================================================
FAIL: Call psw, and do a trivial check on its output.
- -
Traceback (most recent call last):
File "test_Wise.py", line 31, in test_psw
self.assert_(sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))
AssertionError======================================================================
FAIL: Doctest: Bio.Wise._build_align_cmdline
- -
Traceback (most recent call last):
File "/usr/lib/python2.5/doctest.py", line 2128, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.Wise._build_align_cmdline
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 23, in _build_align_cmdline
- -
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 26, in Bio.Wise._build_align_cmdline
Failed example:
_build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), "/tmp/output", kbyte=100000)
Expected:
'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output'
Got:
'dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/output'
- -
File "/home/hogehoge/work/biopython/1.54_stable/biopython-1.54/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 28, in Bio.Wise._build_align_cmdline
Failed example:
_build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), "/tmp/output_aa")
Expected:
'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa'
Got:
'psw -kbyte 300000 -quiet seq1.faa seq2.faa > /tmp/output_aa'
- -
Ran 144 tests in 254.850 seconds
FAILED (failures = 10)
