[Biopython] Installation Help
Tomlin, Joshua James
tomlin.9 at wright.edu
Mon May 13 20:38:35 EDT 2013
I'm trying to install biopython on my laptop. I have mac os x 10.7.5, python 2.7, and have installed numpy I believe.
I can run the 'import Bio' command in python without any errors but when I try run 'python setup.py test' I get 6 errors as seen in the output below:
Basically I need to know if I have done everything I need to do correctly? If I have then why are these 6 tests failing and will that impact my future use of biopython?
Thanks.
Python version: 2.7.4 (v2.7.4:026ee0057e2d, Apr 6 2013, 11:43:10)
[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_BioSQL_MySQLdb ... skipping. Install MySQLdb if you want to use mysql with BioSQL
test_BioSQL_psycopg2 ... skipping. Install psycopg2 if you want to use pg with BioSQL
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 ... skipping. If you want to use Bio.Cluster, install NumPy first and then reinstall Biopython
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_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 ... skipping. C module in Bio.KDTree not compiled
test_KEGG ... ok
test_KeyWList ... ok
test_Location ... ok
test_LogisticRegression ... ok
test_MMCIF ... skipping. C extension MMCIFlex not installed.
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_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_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 ... skipping. C module in Bio.KDTree not compiled
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_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 ... 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/joshtomlin/Downloads/biopython-1.61/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 ... FAIL
test_SeqIO ... ok
test_SeqIO_AbiIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_PdbIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_SeqXML ... ok
test_SeqIO_convert ... ok
test_SeqIO_features ... ok
test_SeqIO_index ... FAIL
test_SeqIO_online ... ok
test_SeqIO_write ... ok
test_SeqRecord ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SffIO ... ok
test_SubsMat ... ok
test_SwissProt ... ok
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
test_TogoWS ... ok
test_Tutorial ... FAIL
test_UniGene ... ok
test_Uniprot ... 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 ... 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 ... ok
test_prosite1 ... ok
test_prosite2 ... 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/joshtomlin/Downloads/biopython-1.61/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/joshtomlin/Downloads/biopython-1.61/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/joshtomlin/Downloads/biopython-1.61/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 ... ok
Bio.KEGG.Enzyme docstring test ... ok
Bio.Motif docstring test ... ok
Bio.Motif.Applications._AlignAce docstring test ... ok
Bio.Motif.Applications._XXmotif docstring test ... ok
Bio.motifs docstring test ... 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 ... 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.Seq docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.FastaIO 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.SeqFeature docstring test ... ok
Bio.SeqRecord docstring test ... 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 34, in test_read_from_url
rec = Entrez.read(einfo)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/Entrez/__init__.py", line 362, in read
record = handler.read(handle)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/Entrez/Parser.py", line 184, in read
self.parser.ParseFile(handle)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/Entrez/Parser.py", line 322, in endElementHandler
raise RuntimeError(value)
RuntimeError: Unable to open connection to #DbInfo?dbaf=
======================================================================
ERROR: test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_SearchIO_write.py", line 55, in test_write_multiple_from_blastxml
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
File "test_SearchIO_write.py", line 27, in parse_write_and_compare
SearchIO.write(source_qresults, out_file, out_format, **kwargs)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SearchIO/__init__.py", line 610, in write
writer.write_file(qresults)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SearchIO/BlastIO/blast_xml.py", line 695, in write_file
xml.startDocument()
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SearchIO/BlastIO/blast_xml.py", line 612, in startDocument
self.write('<?xml version="1.0"?>\n'
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/sax/saxutils.py", line 103, in write
super(UnbufferedTextIOWrapper, self).write(s)
TypeError: must be unicode, not str
======================================================================
ERROR: test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_SearchIO_write.py", line 49, in test_write_single_from_blastxml
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
File "test_SearchIO_write.py", line 27, in parse_write_and_compare
SearchIO.write(source_qresults, out_file, out_format, **kwargs)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SearchIO/__init__.py", line 610, in write
writer.write_file(qresults)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SearchIO/BlastIO/blast_xml.py", line 695, in write_file
xml.startDocument()
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SearchIO/BlastIO/blast_xml.py", line 612, in startDocument
self.write('<?xml version="1.0"?>\n'
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/sax/saxutils.py", line 103, in write
super(UnbufferedTextIOWrapper, self).write(s)
TypeError: must be unicode, not str
======================================================================
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 432, in <lambda>
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 272, in get_raw_check
raw_file = h.read()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 423, in <lambda>
f = lambda x : x.key_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 163, in key_check
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/__init__.py", line 541, in parse
for r in i:
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 1036, in FastqPhredIterator
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 897, in FastqGeneralIterator
line = handle_readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 414, in <lambda>
f = lambda x : x.simple_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 101, in simple_check
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/__init__.py", line 541, in parse
for r in i:
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 1036, in FastqPhredIterator
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 897, in FastqGeneralIterator
line = handle_readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 432, in <lambda>
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 272, in get_raw_check
raw_file = h.read()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 423, in <lambda>
f = lambda x : x.key_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 163, in key_check
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/__init__.py", line 541, in parse
for r in i:
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 1036, in FastqPhredIterator
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 897, in FastqGeneralIterator
line = handle_readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 414, in <lambda>
f = lambda x : x.simple_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 101, in simple_check
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/__init__.py", line 541, in parse
for r in i:
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 1036, in FastqPhredIterator
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/QualityIO.py", line 897, in FastqGeneralIterator
line = handle_readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 432, in <lambda>
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 272, in get_raw_check
raw_file = h.read()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 423, in <lambda>
f = lambda x : x.key_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 163, in key_check
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/__init__.py", line 541, in parse
for r in i:
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 457, in parse_records
record = self.parse(handle, do_features)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 441, in parse
if self.feed(handle, consumer, do_features):
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 398, in feed
if not self.find_start():
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 78, in find_start
line = self.handle.readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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 414, in <lambda>
f = lambda x : x.simple_check(fn, fmt, alpha, c)
File "test_SeqIO_index.py", line 101, in simple_check
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/SeqIO/__init__.py", line 541, in parse
for r in i:
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 457, in parse_records
record = self.parse(handle, do_features)
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 441, in parse
if self.feed(handle, consumer, do_features):
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 398, in feed
if not self.find_start():
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/GenBank/Scanner.py", line 78, in find_start
line = self.handle.readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
ERROR: test_doctests (test_Tutorial.TutorialTestCase)
Run tutorial doctests.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_Tutorial.py", line 152, in test_doctests
ValueError: 4 Tutorial doctests failed: test_from_line_05671, test_from_line_06030, test_from_line_06190, test_from_line_06479
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
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/2.7/lib/python2.7/gzip.py", line 253, in read
while self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
======================================================================
FAIL: bgzf (Bio)
Doctest: Bio.bgzf
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/doctest.py", line 2201, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.bgzf
File "/Users/joshtomlin/Downloads/biopython-1.61/Bio/bgzf.py", line 6, in bgzf
----------------------------------------------------------------------
File "/Users/joshtomlin/Downloads/biopython-1.61/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/2.7/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "<doctest Bio.bgzf[10]>", line 1, in <module>
line = handle.readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
----------------------------------------------------------------------
File "/Users/joshtomlin/Downloads/biopython-1.61/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/2.7/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "<doctest Bio.bgzf[11]>", line 1, in <module>
assert 80 == handle.tell()
AssertionError
----------------------------------------------------------------------
File "/Users/joshtomlin/Downloads/biopython-1.61/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/2.7/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "<doctest Bio.bgzf[12]>", line 1, in <module>
line = handle.readline()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 451, in readline
c = self.read(readsize)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 197, in _read_gzip_header
raise IOError, 'Not a gzipped file'
IOError: Not a gzipped file
----------------------------------------------------------------------
File "/Users/joshtomlin/Downloads/biopython-1.61/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/2.7/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "<doctest Bio.bgzf[13]>", line 1, in <module>
assert 143 == handle.tell()
AssertionError
----------------------------------------------------------------------
File "/Users/joshtomlin/Downloads/biopython-1.61/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/2.7/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "<doctest Bio.bgzf[14]>", line 1, in <module>
data = handle.read(70000)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.py", line 197, in _read_gzip_header
raise IOError, 'Not a gzipped file'
IOError: Not a gzipped file
----------------------------------------------------------------------
File "/Users/joshtomlin/Downloads/biopython-1.61/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/2.7/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "<doctest Bio.bgzf[15]>", line 1, in <module>
assert 70143 == handle.tell()
AssertionError
----------------------------------------------------------------------
Ran 213 tests in 296.686 seconds
FAILED (failures = 6)
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