[Biopython] Problem installing biopython with Python 3.3.1.rc1
Nicolas Joannin
nicolas.joannin at gmail.com
Sat Apr 6 15:31:40 UTC 2013
Hello everyone,
I'm having a problem installing biopython with Python 3.3.1rc1...
Basically, I get several tests failing (in addition to a lot of warnings).
I don't think the failed tests will be a problem for my work, however, I
thought you'd want to have a look... Attached is the output of python3
setup.py test.
Also, if you think I shouldn't use biopython without having these failed
tests fixed first, please let me know!
Best regards,
Nicolas
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Nicolass-MacBook-Air:biopython NicojoAir11$ python3 setup.py test
WARNING - Biopython does not yet officially support Python 3
The 2to3 library will be called automatically now,
and the converted files cached under build/py3.3
Processing Bio
Processing BioSQL
Processing Tests
Processing Scripts
Processing Doc
Python 2to3 processing done.
running test
Python version: 3.3.1rc1 (v3.3.1rc1:92c2cfb92405, Mar 25 2013, 00:54:04)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
Operating system: posix darwin
test_Ace ... ok
test_AlignIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_convert ... ok
test_Application ... ok
test_BioSQL_MySQLdb ... skipping. Install MySQLdb if you want to use mysql with BioSQL
test_BioSQL_psycopg2 ... skipping. Connection failed, check settings if you plan to use BioSQL: FATAL: role "postgres" does not exist
test_BioSQL_sqlite3 ... ok
test_CAPS ... ok
test_Chi2 ... ok
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
test_Cluster ... ok
test_CodonTable ... ok
test_CodonUsage ... ok
test_ColorSpiral ... skipping. Install reportlab if you want to use Bio.Graphics.
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_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_Entrez_online ... FAIL
test_Enzyme ... ok
test_FSSP ... ok
test_Fasttree_tool ... skipping. Install fasttree and correctly set the file path to the program if you want to use it from Biopython.
test_File ... ok
test_GACrossover ... ok
test_GAMutation ... ok
test_GAOrganism ... ok
test_GAQueens ... ok
test_GARepair ... ok
test_GASelection ... ok
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_KDTree ... ok
test_KEGG ... ok
test_KeyWList ... ok
test_Location ... ok
test_LogisticRegression ... ok
test_MMCIF ... skipping. C extension MMCIFlex not installed.
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 ... ok
test_NCBI_qblast ... ok
test_NNExclusiveOr ... ok
test_NNGene ... ok
test_NNGeneral ... ok
test_Nexus ... ok
test_PAML_baseml ... ok
test_PAML_codeml ... ok
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
test_PAML_yn00 ... 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_CDAO ... skipping. Install the librdf Python bindings if you want to use the CDAO tree format.
test_Phylo_NeXML ... ./test_Phylo_NeXML.py:87: ResourceWarning: unclosed file <_io.BufferedReader name='/var/folders/9w/kkwnss4n52bbc3crhctbhfnh0000gn/T/tmpf9__6a'>
t2 = next(NeXMLIO.Parser(open(DUMMY, 'rb')).parse())
ok
test_Phylo_depend ... skipping. Install matplotlib if you want to use Bio.Phylo._utils.
test_PopGen_DFDist ... skipping. Install Dfdist, Ddatacal, pv2 and cplot2 if you want to use DFDist with Bio.PopGen.FDist.
test_PopGen_FDist ... skipping. Install fdist2, datacal, pv and cplot if you want to use FDist2 with 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 ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
test_ProtParam ... ok
test_Restriction ... ok
test_SCOP_Astral ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/__init__.py:672: ResourceWarning: unclosed file <_io.TextIOWrapper name='SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa' mode='r' encoding='UTF-8'>
for record in sequences:
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_SCOP_online ... ok
test_SVDSuperimposer ... ok
test_SearchIO_blast_tab ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SearchIO/__init__.py:213: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
ok
test_SearchIO_blast_tab_index ... ok
test_SearchIO_blast_text ... ok
test_SearchIO_blast_xml ... ok
test_SearchIO_blast_xml_index ... ok
test_SearchIO_blat_psl ... ok
test_SearchIO_blat_psl_index ... ok
test_SearchIO_exonerate ... ok
test_SearchIO_exonerate_text_index ... ok
test_SearchIO_exonerate_vulgar_index ... ok
test_SearchIO_fasta_m10 ... ok
test_SearchIO_fasta_m10_index ... ok
test_SearchIO_hmmer2_text ... ok
test_SearchIO_hmmer2_text_index ... ok
test_SearchIO_hmmer3_domtab ... ok
test_SearchIO_hmmer3_domtab_index ... ok
test_SearchIO_hmmer3_tab ... ok
test_SearchIO_hmmer3_tab_index ... ok
test_SearchIO_hmmer3_text ... ok
test_SearchIO_hmmer3_text_index ... ok
test_SearchIO_model ... ok
test_SearchIO_write ... ok
test_SeqIO ... ok
test_SeqIO_AbiIO ... ok
test_SeqIO_FastaIO ... ./test_SeqIO_FastaIO.py:94: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
re_titled = list(FastaIterator(open(filename), alphabet, title_to_ids))
./test_SeqIO_FastaIO.py:95: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
default = list(SeqIO.parse(open(filename), "fasta", alphabet))
./test_SeqIO_FastaIO.py:94: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/f002' mode='r' encoding='UTF-8'>
re_titled = list(FastaIterator(open(filename), alphabet, title_to_ids))
./test_SeqIO_FastaIO.py:95: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/f002' mode='r' encoding='UTF-8'>
default = list(SeqIO.parse(open(filename), "fasta", alphabet))
./test_SeqIO_FastaIO.py:94: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/fa01' mode='r' encoding='UTF-8'>
re_titled = list(FastaIterator(open(filename), alphabet, title_to_ids))
./test_SeqIO_FastaIO.py:95: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/fa01' mode='r' encoding='UTF-8'>
default = list(SeqIO.parse(open(filename), "fasta", alphabet))
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/centaurea.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/centaurea.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/elderberry.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/elderberry.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/f001' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/f001' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/lavender.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/lavender.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/lupine.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/lupine.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/phlox.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/phlox.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/sweetpea.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/sweetpea.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/wisteria.nu' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/wisteria.nu' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/aster.pro' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/aster.pro' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/loveliesbleeding.pro' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/loveliesbleeding.pro' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/rose.pro' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/rose.pro' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
./test_SeqIO_FastaIO.py:48: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/rosemary.pro' mode='r' encoding='UTF-8'>
second = next(iterator)
./test_SeqIO_FastaIO.py:83: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/rosemary.pro' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(filename), "fasta", alphabet)
ok
test_SeqIO_Insdc ... ok
test_SeqIO_PdbIO ... ok
test_SeqIO_QualityIO ... ./test_SeqIO_QualityIO.py:348: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
records1 = list(SeqIO.parse(open("Quality/example.fasta"),"fasta"))
./test_SeqIO_QualityIO.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fastq' mode='r' encoding='UTF-8'>
records2 = list(SeqIO.parse(open("Quality/example.fastq"),"fastq"))
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:357: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
self.assertEqual(h.getvalue(),open("Quality/example.fasta").read())
./test_SeqIO_QualityIO.py:328: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
open("Quality/example.qual")))
./test_SeqIO_QualityIO.py:328: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='r' encoding='UTF-8'>
open("Quality/example.qual")))
./test_SeqIO_QualityIO.py:329: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fastq' mode='r' encoding='UTF-8'>
records2 = list(SeqIO.parse(open("Quality/example.fastq"),"fastq"))
./test_SeqIO_QualityIO.py:334: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='r' encoding='UTF-8'>
records1 = list(SeqIO.parse(open("Quality/example.qual"),"qual"))
./test_SeqIO_QualityIO.py:335: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fastq' mode='r' encoding='UTF-8'>
records2 = list(SeqIO.parse(open("Quality/example.fastq"),"fastq"))
./test_SeqIO_QualityIO.py:344: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='r' encoding='UTF-8'>
self.assertEqual(h.getvalue(),open("Quality/example.qual").read())
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/illumina_full_range_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/illumina_full_range_original_illumina.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/illumina_full_range_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/illumina_full_range_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/longreads_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/longreads_original_sanger.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/longreads_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/longreads_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_dna_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_dna_original_sanger.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_dna_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_dna_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_rna_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_rna_original_sanger.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_rna_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/misc_rna_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_full_range_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_full_range_original_sanger.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_full_range_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_full_range_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_full_range_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_full_range_original_solexa.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_full_range_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_full_range_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/wrapping_as_sanger.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/wrapping_original_sanger.fastq' mode='r' encoding='UTF-8'>
for record in records:
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/wrapping_as_solexa.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:287: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/wrapping_as_illumina.fastq' mode='rU' encoding='UTF-8'>
"rU").read()
./test_SeqIO_QualityIO.py:223: ResourceWarning: unclosed file <_io.TextIOWrapper name='Roche/E3MFGYR02_random_10_reads_no_trim.fasta' mode='r' encoding='UTF-8'>
wanted = list(SeqIO.parse(open(out_name), format))
./test_SeqIO_QualityIO.py:223: ResourceWarning: unclosed file <_io.TextIOWrapper name='Roche/E3MFGYR02_random_10_reads_no_trim.qual' mode='r' encoding='UTF-8'>
wanted = list(SeqIO.parse(open(out_name), format))
./test_SeqIO_QualityIO.py:223: ResourceWarning: unclosed file <_io.TextIOWrapper name='Roche/E3MFGYR02_random_10_reads.fasta' mode='r' encoding='UTF-8'>
wanted = list(SeqIO.parse(open(out_name), format))
./test_SeqIO_QualityIO.py:223: ResourceWarning: unclosed file <_io.TextIOWrapper name='Roche/E3MFGYR02_random_10_reads.qual' mode='r' encoding='UTF-8'>
wanted = list(SeqIO.parse(open(out_name), format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_random_10_reads.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_alt_index_at_end.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_alt_index_at_start.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_alt_index_in_middle.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_index_at_start.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_index_in_middle.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_no_manifest.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/greek.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/illumina_faked.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/paired.sff'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_93.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_faked.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_example.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_faked.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
./test_SeqIO_QualityIO.py:45: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/tricky.fastq' mode='r' encoding='UTF-8'>
records = list(SeqIO.parse(open(filename, mode),in_format))
ok
test_SeqIO_SeqXML ... ./test_SeqIO_SeqXML.py:141: DeprecationWarning: Please use assertEqual instead.
self.assertEquals(len(read1_records),len(read2_records))
ok
test_SeqIO_convert ... ok
test_SeqIO_features ... ./test_SeqIO_features.py:190: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/iro.gb' mode='rU' encoding='UTF-8'>
gbk_template = open("GenBank/iro.gb", "rU").read()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqFeature.py:155: BiopythonDeprecationWarning: Rather than sub_features, use a CompoundFeatureLocation
BiopythonDeprecationWarning)
./test_SeqIO_features.py:988: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_000932.gb' mode='r' encoding='UTF-8'>
gb_record = SeqIO.read(open(self.gb_filename),"genbank")
./test_SeqIO_features.py:989: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_000932.gb' mode='r' encoding='UTF-8'>
gb_cds = list(SeqIO.parse(open(self.gb_filename),"genbank-cds"))
./test_SeqIO_features.py:990: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_000932.faa' mode='r' encoding='UTF-8'>
fasta = list(SeqIO.parse(open(self.faa_filename),"fasta"))
./test_SeqIO_features.py:988: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
gb_record = SeqIO.read(open(self.gb_filename),"genbank")
./test_SeqIO_features.py:989: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
gb_cds = list(SeqIO.parse(open(self.gb_filename),"genbank-cds"))
./test_SeqIO_features.py:990: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.faa' mode='r' encoding='UTF-8'>
fasta = list(SeqIO.parse(open(self.faa_filename),"fasta"))
./test_SeqIO_features.py:1070: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
gb_record = SeqIO.read(open(self.gb_filename),"genbank")
./test_SeqIO_features.py:1072: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.ffn' mode='r' encoding='UTF-8'>
fa_records = list(SeqIO.parse(open(self.ffn_filename),"fasta"))
./test_SeqIO_features.py:1023: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
gb_record = SeqIO.read(open(self.gb_filename),"genbank")
./test_SeqIO_features.py:1024: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/AE017046.embl' mode='r' encoding='UTF-8'>
embl_record = SeqIO.read(open(self.embl_filename),"embl")
./test_SeqIO_features.py:1054: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
gb_record = SeqIO.read(open(self.gb_filename),"genbank")
./test_SeqIO_features.py:1055: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.fna' mode='r' encoding='UTF-8'>
fa_record = SeqIO.read(open(self.fna_filename),"fasta")
./test_SeqIO_features.py:1059: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/AE017046.embl' mode='r' encoding='UTF-8'>
embl_record = SeqIO.read(open(self.embl_filename),"embl")
./test_SeqIO_features.py:1036: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.faa' mode='r' encoding='UTF-8'>
faa_records = list(SeqIO.parse(open(self.faa_filename),"fasta"))
./test_SeqIO_features.py:1037: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.ffn' mode='r' encoding='UTF-8'>
ffn_records = list(SeqIO.parse(open(self.ffn_filename),"fasta"))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/AAA03323.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/AE017046.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/DD231055_edited.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/Human_contigs.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_000932.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NT_019265.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/SC10H5.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/TRBG361.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='EMBL/U87107.embl' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/arab1.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/blank_seq.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/cor6_6.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/dbsource_wrap.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/extra_keywords.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/gbvrl1_start.seq' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/noref.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/one_of.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/origin_line.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/pri1.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/protein_refseq.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
./test_SeqIO_features.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/protein_refseq2.gb' mode='r' encoding='UTF-8'>
gb_records = list(SeqIO.parse(open(filename),in_format))
ok
test_SeqIO_index ... FAIL
test_SeqIO_online ... ok
test_SeqIO_write ... ok
test_SeqRecord ... ok
test_SeqUtils ... ./test_SeqUtils.py:71: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
record = SeqIO.read(open(dna_genbank_filename), "genbank")
./test_SeqUtils.py:55: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/f002' mode='r' encoding='UTF-8'>
seq_records = list(SeqIO.parse(open(dna_fasta_filename), "fasta"))
ok
test_Seq_objs ... ok
test_SffIO ... ok
test_SubsMat ... ./test_SubsMat.py:21: ResourceWarning: unclosed file <_io.TextIOWrapper name='SubsMat/protein_count.txt' mode='r' encoding='UTF-8'>
ftab_prot = FreqTable.read_count(open(ftab_file))
./test_SubsMat.py:23: ResourceWarning: unclosed file <_io.TextIOWrapper name='SubsMat/protein_freq.txt' mode='r' encoding='UTF-8'>
ctab_prot = FreqTable.read_freq(open(ctab_file))
./test_SubsMat.py:31: ResourceWarning: unclosed file <_io.BufferedReader name='SubsMat/acc_rep_mat.pik'>
acc_rep_mat = pickle.load(open(pickle_file, 'rb'))
ok
test_SwissProt ... ok
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
test_TogoWS ... ./test_TogoWS.py:501: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
new = SeqIO.read(TogoWS.convert(open(filename), "genbank", "embl"), "embl")
./test_TogoWS.py:494: ResourceWarning: unclosed file <_io.TextIOWrapper name='GenBank/NC_005816.gb' mode='r' encoding='UTF-8'>
new = SeqIO.read(TogoWS.convert(open(filename), "genbank", "fasta"), "fasta")
ok
test_Tutorial ... /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.BufferedReader name='ls_orchid.gbk'>
test.globs.clear()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.BufferedReader name='ls_orchid.gbk.bgz'>
test.globs.clear()
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='tab_2226_tblastn_001.txt'>
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='tab_2226_tblastn_005.txt'>
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.BufferedReader name='tab_2226_tblastn_001.txt'>
test.globs.clear()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.TextIOWrapper name='pubmed_result1.txt' mode='r' encoding='UTF-8'>
test.globs.clear()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.TextIOWrapper name='pubmed_result2.txt' mode='r' encoding='UTF-8'>
test.globs.clear()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.TextIOWrapper name='lipoprotein.txt' mode='r' encoding='UTF-8'>
test.globs.clear()
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Arnt.sites' mode='r' encoding='UTF-8'>
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='SRF.pfm' mode='r' encoding='UTF-8'>
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='REB1.pfm' mode='r' encoding='UTF-8'>
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1439: ResourceWarning: unclosed file <_io.TextIOWrapper name='Arnt.sites' mode='r' encoding='UTF-8'>
test.globs.clear()
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='meme.out' mode='r' encoding='UTF-8'>
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='alignace.out' mode='r' encoding='UTF-8'>
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Arnt.sites' mode='r' encoding='UTF-8'>
./test_Tutorial.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='SRF.pfm' mode='r' encoding='UTF-8'>
ok
test_UniGene ... ok
test_Uniprot ... ./test_Uniprot.py:314: ResourceWarning: unclosed file <_io.TextIOWrapper name='SwissProt/multi_ex.list' mode='r' encoding='UTF-8'>
ids = [x.strip() for x in open("SwissProt/multi_ex.list")]
./test_Uniprot.py:328: ResourceWarning: unclosed file <_io.TextIOWrapper name='SwissProt/multi_ex.list' mode='r' encoding='UTF-8'>
ids = [x.strip() for x in open("SwissProt/multi_ex.list")]
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.BufferedReader name='SwissProt/multi_ex.txt'>
function()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.BufferedReader name='SwissProt/multi_ex.xml'>
function()
ok
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
test_align ... ok
test_bgzf ... FAIL
test_geo ... ./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/GSE16.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/GSM645.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/GSM691.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/GSM700.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/GSM804.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/soft_ex_affy.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/soft_ex_affy_chp.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/soft_ex_dual.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/soft_ex_family.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
./test_geo.py:24: ResourceWarning: unclosed file <_io.TextIOWrapper name='Geo/soft_ex_platform.txt' mode='r' encoding='latin'>
fh = open(os.path.join("Geo", file), encoding="latin")
ok
test_kNN ... ok
test_lowess ... ok
test_motifs ... ok
test_pairwise2 ... ok
test_phyml_tool ... skipping. Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper.
test_prodoc ... /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/Doc/prosite.excerpt.doc' mode='r' encoding='UTF-8'>
function()
ok
test_prosite1 ... /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/ps00107.txt' mode='r' encoding='UTF-8'>
function()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/ps00159.txt' mode='r' encoding='UTF-8'>
function()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/ps00165.txt' mode='r' encoding='UTF-8'>
function()
ok
test_prosite2 ... /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/ps00432.txt' mode='r' encoding='UTF-8'>
function()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/ps00488.txt' mode='r' encoding='UTF-8'>
function()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/unittest/case.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='Prosite/ps00546.txt' mode='r' encoding='UTF-8'>
function()
ok
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_py3k ... ok
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
test_seq ... ok
test_translate ... ok
test_trie ... skipping. Could not import Bio.trie, check C code was compiled.
Bio.Align docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.Align.Applications._Clustalw docstring test ... ok
Bio.Align.Applications._ClustalOmega docstring test ... ok
Bio.Align.Applications._Mafft docstring test ... ok
Bio.Align.Applications._Muscle docstring test ... ok
Bio.Align.Applications._Probcons docstring test ... ok
Bio.Align.Applications._Prank docstring test ... ok
Bio.Align.Applications._TCoffee docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Alphabet docstring test ... ok
Bio.Application docstring test ... ok
Bio.bgzf docstring test ... FAIL
Bio.Blast.Applications docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Blast/Applications.py:218: BiopythonDeprecationWarning: Like blastall, this wrapper is now deprecated and will be removed in a future release of Biopython.
warnings.warn("Like blastall, this wrapper is now deprecated and will be removed in a future release of Biopython.", BiopythonDeprecationWarning)
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Blast/Applications.py:321: BiopythonDeprecationWarning: Like blastpgp (and blastall), this wrapper is now deprecated and will be removed in a future release of Biopython.
warnings.warn("Like blastpgp (and blastall), this wrapper is now deprecated and will be removed in a future release of Biopython.", BiopythonDeprecationWarning)
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Blast/Applications.py:400: BiopythonDeprecationWarning: Like the old rpsblast (and blastall), this wrapper is now deprecated and will be removed in a future release of Biopython.
warnings.warn("Like the old rpsblast (and blastall), this wrapper is now deprecated and will be removed in a future release of Biopython.", BiopythonDeprecationWarning)
ok
Bio.Emboss.Applications docstring test ... ok
Bio.GenBank docstring test ... ok
Bio.KEGG.Compound docstring test ... /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.TextIOWrapper name='KEGG/compound.sample' mode='r' encoding='UTF-8'>
test.globs.clear()
ok
Bio.KEGG.Enzyme docstring test ... /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.TextIOWrapper name='KEGG/enzyme.sample' mode='r' encoding='UTF-8'>
test.globs.clear()
ok
Bio.Motif docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Motif/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Motif/alignace.out' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Motif/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Motif/SRF.pfm' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Motif/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Motif/meme.out' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1289: ResourceWarning: unclosed file <_io.TextIOWrapper name='Motif/alignace.out' mode='r' encoding='UTF-8'>
exception = None
ok
Bio.Motif.Applications._AlignAce docstring test ... ok
Bio.Motif.Applications._XXmotif docstring test ... ok
Bio.motifs docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/motifs/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Motif/alignace.out' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/motifs/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='motifs/SRF.pfm' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/motifs/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='motifs/meme.out' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:1289: ResourceWarning: unclosed file <_io.TextIOWrapper name='motifs/alignace.out' mode='r' encoding='UTF-8'>
exception = None
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/motifs/__init__.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='motifs/alignace.out' mode='r' encoding='UTF-8'>
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
ok
Bio.motifs.applications._alignace docstring test ... ok
Bio.motifs.applications._xxmotif docstring test ... ok
Bio.pairwise2 docstring test ... ok
Bio.Phylo.Applications._Raxml docstring test ... ok
Bio.SearchIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SearchIO/__init__.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Blast/wnts.xml'>
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SearchIO/__init__.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Blast/wnts.xml.bgz'>
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='Blast/wnts.xml'>
test.globs.clear()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SearchIO/__init__.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Blast/mirna.xml'>
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='Blast/mirna.xml'>
test.globs.clear()
ok
Bio.SearchIO._model docstring test ... ok
Bio.SearchIO._model.query docstring test ... ok
Bio.SearchIO._model.hit docstring test ... ok
Bio.SearchIO._model.hsp docstring test ... ok
Bio.SearchIO.BlastIO docstring test ... ok
Bio.SearchIO.HmmerIO docstring test ... ok
Bio.SearchIO.FastaIO docstring test ... ok
Bio.SearchIO.BlatIO docstring test ... ok
Bio.SearchIO.ExonerateIO docstring test ... ok
Bio.SeqIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/__init__.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Fasta/f002'>
# Copyright 2006-2010 by Peter Cock. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='Fasta/f002'>
test.globs.clear()
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/__init__.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Quality/example.fastq'>
# Copyright 2006-2010 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/__init__.py:672: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fastq' mode='r' encoding='UTF-8'>
for record in sequences:
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/__init__.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Quality/example.fastq.bgz'>
# Copyright 2006-2010 by Peter Cock. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='Quality/example.fastq'>
test.globs.clear()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='GenBank/NC_000932.faa'>
test.globs.clear()
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='GenBank/NC_005816.faa'>
test.globs.clear()
ok
Bio.SeqIO.FastaIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/FastaIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/dups.fasta' mode='r' encoding='UTF-8'>
# Copyright 2006-2009 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/FastaIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/dups.fasta' mode='r' encoding='UTF-8'>
# Copyright 2006-2009 by Peter Cock. All rights reserved.
ok
Bio.SeqIO.AceIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/AceIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Ace/consed_sample.ace' mode='rU' encoding='UTF-8'>
# Copyright 2008-2010 by Peter Cock. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.TextIOWrapper name='Ace/contig1.ace' mode='rU' encoding='UTF-8'>
test.globs.clear()
ok
Bio.SeqIO.PhdIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/PhdIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Phd/phd1' mode='r' encoding='UTF-8'>
# Copyright 2008-2010 by Peter Cock. All rights reserved.
ok
Bio.SeqIO.QualityIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/__init__.py:672: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='r' encoding='UTF-8'>
for record in sequences:
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/QualityIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='r' encoding='UTF-8'>
# Copyright 2009-2010 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/QualityIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/illumina_faked.fastq' mode='r' encoding='UTF-8'>
# Copyright 2009-2010 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/QualityIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/sanger_faked.fastq' mode='r' encoding='UTF-8'>
# Copyright 2009-2010 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_example.fastq' mode='r' encoding='UTF-8'>
for record in records:
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/QualityIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='rU' encoding='UTF-8'>
# Copyright 2009-2010 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/QualityIO.py:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='rU' encoding='UTF-8'>
# Copyright 2009-2010 by Peter Cock. All rights reserved.
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.fasta' mode='rU' encoding='UTF-8'>
for record in records:
/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/Interfaces.py:238: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/example.qual' mode='rU' encoding='UTF-8'>
for record in records:
ok
./run_tests.py:427: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_faked.fastq' mode='r' encoding='UTF-8'>
gc.collect()
Bio.SeqIO.SffIO docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqIO/SffIO.py:1: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_random_10_reads.sff'>
# Copyright 2009-2010 by Peter Cock. All rights reserved.
/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py:2130: ResourceWarning: unclosed file <_io.BufferedReader name='Roche/E3MFGYR02_random_10_reads.sff'>
test.globs.clear()
ok
Bio.SeqFeature docstring test ... ok
Bio.SeqRecord docstring test ... /Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/SeqRecord.py:2: ResourceWarning: unclosed file <_io.TextIOWrapper name='Quality/solexa_faked.fastq' mode='rU' encoding='UTF-8'>
# Copyright 2002-2004 Brad Chapman.
ok
Bio.SeqUtils docstring test ... ok
Bio.SeqUtils.MeltingTemp docstring test ... ok
Bio.Sequencing.Applications._Novoalign docstring test ... ok
Bio.Wise docstring test ... ok
Bio.Wise.psw docstring test ... ok
Bio.Statistics.lowess docstring test ... ok
Bio.PDB.Polypeptide docstring test ... ok
Bio.PDB.Selection docstring test ... ok
======================================================================
ERROR: test_read_from_url (test_Entrez_online.EntrezOnlineCase)
Test Entrez.read from URL
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_Entrez_online.py", line 44, in test_read_from_url
rec = Entrez.read(einfo)
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Entrez/__init__.py", line 367, in read
record = handler.read(handle)
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Entrez/Parser.py", line 184, in read
self.parser.ParseFile(handle)
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/Entrez/Parser.py", line 322, in endElementHandler
raise RuntimeError(value)
RuntimeError: Unable to open connection to #DbInfo?dbaf=
======================================================================
ERROR: test_fastq-sanger_Quality_example_fastq_bgz_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq.bgz get_raw
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 441, in <lambda>
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 281, in get_raw_check
raw_file = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_fastq-sanger_Quality_example_fastq_bgz_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq.bgz with key function
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 432, in <lambda>
f = lambda x : x.key_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 171, in key_check
h = gzip_open(filename, format)
File "./test_SeqIO_index.py", line 49, in gzip_open
data = handle.read() # bytes!
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_fastq-sanger_Quality_example_fastq_bgz_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq.bgz defaults
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 423, in <lambda>
f = lambda x : x.simple_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 109, in simple_check
h = gzip_open(filename, format)
File "./test_SeqIO_index.py", line 49, in gzip_open
data = handle.read() # bytes!
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_fastq_Quality_example_fastq_bgz_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq.bgz get_raw
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 441, in <lambda>
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 281, in get_raw_check
raw_file = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_fastq_Quality_example_fastq_bgz_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq.bgz with key function
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 432, in <lambda>
f = lambda x : x.key_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 171, in key_check
h = gzip_open(filename, format)
File "./test_SeqIO_index.py", line 49, in gzip_open
data = handle.read() # bytes!
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_fastq_Quality_example_fastq_bgz_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq.bgz defaults
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 423, in <lambda>
f = lambda x : x.simple_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 109, in simple_check
h = gzip_open(filename, format)
File "./test_SeqIO_index.py", line 49, in gzip_open
data = handle.read() # bytes!
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_genbank_GenBank_cor6_6_gb_bgz_get_raw (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb.bgz get_raw
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 441, in <lambda>
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 281, in get_raw_check
raw_file = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_genbank_GenBank_cor6_6_gb_bgz_keyf (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb.bgz with key function
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 432, in <lambda>
f = lambda x : x.key_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 171, in key_check
h = gzip_open(filename, format)
File "./test_SeqIO_index.py", line 49, in gzip_open
data = handle.read() # bytes!
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_genbank_GenBank_cor6_6_gb_bgz_simple (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb.bgz defaults
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_SeqIO_index.py", line 423, in <lambda>
f = lambda x : x.simple_check(fn, fmt, alpha, c)
File "./test_SeqIO_index.py", line 109, in simple_check
h = gzip_open(filename, format)
File "./test_SeqIO_index.py", line 49, in gzip_open
data = handle.read() # bytes!
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_bam_ex1 (test_bgzf.BgzfTests)
Reproduce BGZF compression for BAM file
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 288, in test_bam_ex1
self.rewrite("SamBam/ex1.bam", temp_file)
File "./test_bgzf.py", line 34, in rewrite
data = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_example_cor6 (test_bgzf.BgzfTests)
Reproduce BGZF compression for cor6_6.gb GenBank file
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 313, in test_example_cor6
self.rewrite("GenBank/cor6_6.gb.bgz", temp_file)
File "./test_bgzf.py", line 34, in rewrite
data = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_example_fastq (test_bgzf.BgzfTests)
Reproduce BGZF compression for a FASTQ file
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 301, in test_example_fastq
self.rewrite("Quality/example.fastq.gz", temp_file)
File "./test_bgzf.py", line 45, in rewrite
new_data = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_example_gb (test_bgzf.BgzfTests)
Reproduce BGZF compression for NC_000932 GenBank file
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 307, in test_example_gb
self.rewrite("GenBank/NC_000932.gb.bgz", temp_file)
File "./test_bgzf.py", line 34, in rewrite
data = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_example_wnts_xml (test_bgzf.BgzfTests)
Reproduce BGZF compression for wnts.xml BLAST file
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 319, in test_example_wnts_xml
self.rewrite("Blast/wnts.xml.bgz", temp_file)
File "./test_bgzf.py", line 34, in rewrite
data = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_iter_bam_ex1 (test_bgzf.BgzfTests)
Check iteration over SamBam/ex1.bam
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 296, in test_iter_bam_ex1
self.check_by_char("SamBam/ex1.bam", "SamBam/ex1.bam", True)
File "./test_bgzf.py", line 112, in check_by_char
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_random_bam_ex1 (test_bgzf.BgzfTests)
Check random access to SamBam/ex1.bam
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 232, in test_random_bam_ex1
self.check_random("SamBam/ex1.bam")
File "./test_bgzf.py", line 145, in check_random
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_random_bam_ex1_header (test_bgzf.BgzfTests)
Check random access to SamBam/ex1_header.bam
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 240, in test_random_bam_ex1_header
self.check_random("SamBam/ex1_header.bam")
File "./test_bgzf.py", line 145, in check_random
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_random_bam_ex1_refresh (test_bgzf.BgzfTests)
Check random access to SamBam/ex1_refresh.bam
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 236, in test_random_bam_ex1_refresh
self.check_random("SamBam/ex1_refresh.bam")
File "./test_bgzf.py", line 145, in check_random
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_random_example_cor6 (test_bgzf.BgzfTests)
Check random access to GenBank/cor6_6.gb.bgz
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 252, in test_random_example_cor6
self.check_random("GenBank/cor6_6.gb.bgz")
File "./test_bgzf.py", line 145, in check_random
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_random_example_fastq (test_bgzf.BgzfTests)
Check random access to Quality/example.fastq.bgz
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 248, in test_random_example_fastq
self.check_random("Quality/example.fastq.bgz")
File "./test_bgzf.py", line 145, in check_random
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
ERROR: test_random_wnts_xml (test_bgzf.BgzfTests)
Check random access to Blast/wnts.xml.bgz
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_bgzf.py", line 244, in test_random_wnts_xml
self.check_random("Blast/wnts.xml.bgz")
File "./test_bgzf.py", line 145, in check_random
old = h.read()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 359, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
======================================================================
FAIL: bgzf (Bio)
Doctest: Bio.bgzf
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 2154, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.bgzf
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 6, in bgzf
----------------------------------------------------------------------
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 126, in Bio.bgzf
Failed example:
line = handle.readline()
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 1287, in __run
compileflags, 1), test.globs)
File "<doctest Bio.bgzf[10]>", line 1, in <module>
line = handle.readline()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 593, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 364, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 305, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 282, in _read_exact
data = self.fileobj.read(n)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 81, in read
return self.file.read(size)
TypeError: integer argument expected, got 'tuple'
----------------------------------------------------------------------
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 127, in Bio.bgzf
Failed example:
assert 80 == handle.tell()
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 1287, in __run
compileflags, 1), test.globs)
File "<doctest Bio.bgzf[11]>", line 1, in <module>
assert 80 == handle.tell()
AssertionError
----------------------------------------------------------------------
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 128, in Bio.bgzf
Failed example:
line = handle.readline()
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 1287, in __run
compileflags, 1), test.globs)
File "<doctest Bio.bgzf[12]>", line 1, in <module>
line = handle.readline()
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 593, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 364, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 297, in _read_gzip_header
raise IOError('Not a gzipped file')
OSError: Not a gzipped file
----------------------------------------------------------------------
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 129, in Bio.bgzf
Failed example:
assert 143 == handle.tell()
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 1287, in __run
compileflags, 1), test.globs)
File "<doctest Bio.bgzf[13]>", line 1, in <module>
assert 143 == handle.tell()
AssertionError
----------------------------------------------------------------------
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 130, in Bio.bgzf
Failed example:
data = handle.read(70000)
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 1287, in __run
compileflags, 1), test.globs)
File "<doctest Bio.bgzf[14]>", line 1, in <module>
data = handle.read(70000)
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 364, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 432, in _read
if not self._read_gzip_header():
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/gzip.py", line 297, in _read_gzip_header
raise IOError('Not a gzipped file')
OSError: Not a gzipped file
----------------------------------------------------------------------
File "/Users/NicojoAir11/Downloads/biopython/build/py3.3/build/lib.macosx-10.6-intel-3.3/Bio/bgzf.py", line 131, in Bio.bgzf
Failed example:
assert 70143 == handle.tell()
Exception raised:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/doctest.py", line 1287, in __run
compileflags, 1), test.globs)
File "<doctest Bio.bgzf[15]>", line 1, in <module>
assert 70143 == handle.tell()
AssertionError
----------------------------------------------------------------------
Ran 217 tests in 238.221 seconds
FAILED (failures = 4)
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