biopython1.55beta をテストしてみる
dnalがない状態でテストを実行してみた。
biopython-1.55b% dnal zsh: command not found: dnal
LANG=C
なら問題なかった
running test test_Ace ... ok test_AlignIO ... ok test_AlignIO_convert ... ok test_BioSQL ... /home/manabu/work/biopython/1.55beta/biopython-1.55b/build/lib.linux-x86_64-2.5/BioSQL/Loader.py:799: UserWarning: order location operators are not fully supported % feature.location_operator) ok test_BioSQL_SeqIO ... /home/manabu/work/biopython/1.55beta/biopython-1.55b/build/lib.linux-x86_64-2.5/BioSQL/Loader.py:799: UserWarning: bond location operators are not fully supported % feature.location_operator) ok test_CAPS ... ok test_Clustalw ... ok test_Clustalw_tool ... ok 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 ... ok test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools. 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 ... ok test_MarkovModel ... ok test_Medline ... ok test_Motif ... ok test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 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 ... ok test_NNExclusiveOr ... ok test_NNGene ... ok test_NNGeneral ... ok test_Nexus ... ok test_PDB ... ok test_PDB_KDTree ... 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 ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. test_Probcons_tool ... ok 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 ... ok test_UniGene ... ok test_UniGene_obsolete ... ok test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise. test_align ... ok test_geo ... 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 ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise. 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 ... ok Bio.Wise.psw docstring test ... ok Bio.Motif docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok ---------------------------------------------------------------------- Ran 145 tests in 263.285 seconds
しかし
LANG=ja_JP.UTF-8
だと
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ERROR: Call dnal with optional arguments, and do a trivial check on the output.
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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/manabu/work/biopython/1.55beta/biopython-1.55b/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 109, in align
return align(cmdline, pair, 0, force_type, dry_run, quiet, debug)
File "/home/manabu/work/biopython/1.55beta/biopython-1.55b/build/lib.linux-x86_64-2.5/Bio/Wise/__init__.py", line 111, in align
raise OSError("%s returned %s" % (" ".join(cmdline), status))
OSError: dnal returned 127
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Ran 145 tests in 251.877 seconds
FAILED (failures = 1)
