[Biopython] Biopython and Snow Leopard

[Kelly F Oakeson]

Peter,
After installing NumPy everything tests out ok. Here are the results.

$ python setup.py test
running test
test_Ace ... ok
test_AlignIO ... ok
test_BioSQL ... skipping. Enter your settings in Tests/setup_BioSQL.py  
(not important if you do not plan to use BioSQL).
test_BioSQL_SeqIO ... skipping. Enter your settings in Tests/ 
setup_BioSQL.py (not important if you do not plan to use BioSQL).
test_CAPS ... ok
test_Clustalw ... ok
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you  
want to use Bio.Clustalw.
test_Cluster ... ok
test_CodonTable ... ok
test_CodonUsage ... ok
test_Compass ... ok
test_Crystal ... ok
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use  
the Bio.Align.Applications wrapper.
test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.EMBOSS.
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_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 ... skipping. Install MUSCLE if you want to use the  
Bio.Align.Applications wrapper.
test_NCBIStandalone ... ok
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_qblast ... ok
test_NNExclusiveOr ... ok
test_NNGene ... ok
test_NNGeneral ... ok
test_Nexus ... ok
test_PDB ... ok
test_PDB_unit ... ok
test_ParserSupport ... ok
test_Pathway ... ok
test_Phd ... ok
test_PopGen_FDist ... skipping. Install FDist if you want to use  
Bio.PopGen.FDist.
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... 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 ... skipping. Install PROBCONS if you want to use  
the Bio.Align.Applications wrapper.
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_features ... ok
test_SeqIO_online ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SubsMat ... ok
test_SwissProt ... ok
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the  
Bio.Align.Applications wrapper.
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_interpro ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... 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.Seq docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Application 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
----------------------------------------------------------------------
Ran 125 tests in 63.582 seconds
On Sep 9, 2009, at 10:35 AM, Peter wrote:

> On Wed, Sep 9, 2009 at 5:26 PM, Kelly F  
> Oakeson<kelly.oakeson at utah.edu> wrote:
>> Peter,
>> I only ran the setup.py test, but here are the results:
>> $ python setup.py test
>> running test
>> test_Ace ... ok
>> test_AlignIO ... ok
>> test_BioSQL ... skipping. Enter your settings in Tests/ 
>> setup_BioSQL.py
>> (not important if you do not plan to use BioSQL).
>> test_BioSQL_SeqIO ... skipping. Enter your settings in Tests/
>> setup_BioSQL.py (not important if you do not plan to use BioSQL).
>> test_CAPS ... ok
>> test_Clustalw ... ok
>> test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you
>> want to use Bio.Clustalw.
>> test_Cluster ... skipping. If you want to use Bio.Cluster, install
>> NumPy first and then reinstall Biopython
>> ...
>> Bio.Wise.psw docstring test ... ok
>> Bio.Motif docstring test ... ok
>> ----------------------------------------------------------------------
>> Ran 124 tests in 62.858 seconds
>
> Excellent - a clean bill of health.
>
> Do you want to try installing NumPy now, and then reinstalling
> Biopython to see if everything works? ;)
>
> Peter