jamescasbon/PyVCF — pull request #54 by msabramo (2012-06-25 17:32:02+00:00)
Title: Add support for tox (http://tox.testrun.org/)

Output of tox:

```
[last: 0] marca@SCML-MarcA:~/dev/git-repos/PyVCF$ tox
GLOB sdist-make: /Users/marca/dev/git-repos/PyVCF/setup.py
py26 sdist-reinst: /Users/marca/dev/git-repos/PyVCF/.tox/dist/PyVCF-0.5.0-pre.zip
py26 runtests: commands[0]
running test
running build_py
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
running egg_info
writing requirements to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/requires.txt
writing /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/PKG-INFO
writing top-level names to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/top_level.txt
writing dependency_links to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/dependency_links.txt
writing entry points to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/entry_points.txt
reading manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
writing manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
running build_ext
Doctest: vcf ... ok
testCalls (vcf.test.test_vcf.TestGatkOutput) ... ok
testFormats (vcf.test.test_vcf.TestGatkOutput) ... ok
testInfos (vcf.test.test_vcf.TestGatkOutput) ... ok
testSamples (vcf.test.test_vcf.TestGatkOutput) ... ok
testCalls (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testFormats (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testInfos (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestFreebayesOutput) ... ['BLANK', 'NA12878', 'NA12891', 'NA12892', 'NA19238', 'NA19239', 'NA19240']
ok
testSamples (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestSamtoolsOutput) ... ok
testWrite (vcf.test.test_vcf.TestWriter) ... ok
testFetchRange (vcf.test.test_vcf.TestTabix) ... ok
testFetchSite (vcf.test.test_vcf.TestTabix) ... ok
testOpenFilehandle (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilehandleGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilename (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilenameGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testApplyFilter (vcf.test.test_vcf.TestFilter) ... ok
testApplyMultipleFilters (vcf.test.test_vcf.TestFilter) ... ok
testParse (vcf.test.test_vcf.Test1kg) ... ok
docstring for test_issue_49 ... ok
test_aaf (vcf.test.test_vcf.TestRecord) ... ok
test_call_rate (vcf.test.test_vcf.TestRecord) ... ok
test_is_deletion (vcf.test.test_vcf.TestRecord) ... ok
test_is_indel (vcf.test.test_vcf.TestRecord) ... ok
test_is_snp (vcf.test.test_vcf.TestRecord) ... Record(CHROM=20, POS=14370, REF=G, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[51, 51], DP=1, GQ=48)
Call(sample=NA00002, GT=1|0, HQ=[51, 51], DP=8, GQ=48)
Call(sample=NA00003, GT=1/1, HQ=[None, None], DP=5, GQ=43)
Record(CHROM=20, POS=17330, REF=T, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[58, 50], DP=3, GQ=49)
Call(sample=NA00002, GT=0|1, HQ=[65, 3], DP=5, GQ=3)
Call(sample=NA00003, GT=0/0, HQ=None, DP=3, GQ=41)
Record(CHROM=20, POS=1110696, REF=A, ALT=[G, T])
Call(sample=NA00001, GT=1|2, HQ=[23, 27], DP=6, GQ=21)
Call(sample=NA00002, GT=2|1, HQ=[18, 2], DP=0, GQ=2)
Call(sample=NA00003, GT=2/2, HQ=None, DP=4, GQ=35)
Record(CHROM=20, POS=1230237, REF=T, ALT=[None])
Call(sample=NA00001, GT=0|0, HQ=[56, 60], DP=7, GQ=54)
Call(sample=NA00002, GT=0|0, HQ=[51, 51], DP=4, GQ=48)
Call(sample=NA00003, GT=0/0, HQ=None, DP=2, GQ=61)
Record(CHROM=20, POS=1234567, REF=GTCT, ALT=[G, GTACT])
Call(sample=NA00001, GT=None, DP=4, GQ=35)
Call(sample=NA00002, GT=0/2, DP=2, GQ=17)
Call(sample=NA00003, GT=1/1, DP=3, GQ=40)
ok
test_is_sv (vcf.test.test_vcf.TestRecord) ... ok
test_is_sv_precise (vcf.test.test_vcf.TestRecord) ... ok
test_is_transition (vcf.test.test_vcf.TestRecord) ... ok
test_num_calls (vcf.test.test_vcf.TestRecord) ... ok
test_pi (vcf.test.test_vcf.TestRecord) ... ok
test_qual (vcf.test.test_vcf.TestRecord) ... ok
test_sv_end (vcf.test.test_vcf.TestRecord) ... ok
test_var_subtype (vcf.test.test_vcf.TestRecord) ... ok
test_var_type (vcf.test.test_vcf.TestRecord) ... ok
test_gt_bases (vcf.test.test_vcf.TestCall) ... ok
test_gt_types (vcf.test.test_vcf.TestCall) ... {'GT': '0|0', 'HQ': [51, 51], 'DP': 1, 'GQ': 48}
{'GT': '1|0', 'HQ': [51, 51], 'DP': 8, 'GQ': 48}
{'GT': '1/1', 'HQ': [None, None], 'DP': 5, 'GQ': 43}
{'GT': '0|0', 'HQ': [58, 50], 'DP': 3, 'GQ': 49}
{'GT': '0|1', 'HQ': [65, 3], 'DP': 5, 'GQ': 3}
{'GT': '0/0', 'HQ': None, 'DP': 3, 'GQ': 41}
{'GT': '1|2', 'HQ': [23, 27], 'DP': 6, 'GQ': 21}
{'GT': '2|1', 'HQ': [18, 2], 'DP': 0, 'GQ': 2}
{'GT': '2/2', 'HQ': None, 'DP': 4, 'GQ': 35}
{'GT': '0|0', 'HQ': [56, 60], 'DP': 7, 'GQ': 54}
{'GT': '0|0', 'HQ': [51, 51], 'DP': 4, 'GQ': 48}
{'GT': '0/0', 'HQ': None, 'DP': 2, 'GQ': 61}
{'GT': None, 'DP': 4, 'GQ': 35}
{'GT': '0/2', 'DP': 2, 'GQ': 17}
{'GT': '1/1', 'DP': 3, 'GQ': 40}
ok
test_phased (vcf.test.test_vcf.TestCall) ... ok
test_issue_16 (vcf.test.test_vcf.TestRegression) ... ok
test_null_mono (vcf.test.test_vcf.TestRegression) ... /Users/marca/dev/git-repos/PyVCF/build/lib/vcf/test/null_genotype_mono.vcf
##fileformat=VCFv4.1
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[np_control.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[tests/read_chr.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=info log_to_file=null help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig={'length': '249250621', 'assembly': 'hg19', 'ID': 'chr1'}
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##contig={'length': '547496', 'assembly': 'hg19', 'ID': 'chr1_gl000192_random'}
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##contig={'length': '4622290', 'assembly': 'hg19', 'ID': 'chr6_apd_hap1'}
##contig={'length': '4795371', 'assembly': 'hg19', 'ID': 'chr6_cox_hap2'}
##contig={'length': '4610396', 'assembly': 'hg19', 'ID': 'chr6_dbb_hap3'}
##contig={'length': '4683263', 'assembly': 'hg19', 'ID': 'chr6_mann_hap4'}
##contig={'length': '4833398', 'assembly': 'hg19', 'ID': 'chr6_mcf_hap5'}
##contig={'length': '4611984', 'assembly': 'hg19', 'ID': 'chr6_qbl_hap6'}
##contig={'length': '4928567', 'assembly': 'hg19', 'ID': 'chr6_ssto_hap7'}
##contig={'length': '159138663', 'assembly': 'hg19', 'ID': 'chr7'}
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##contig={'length': '38914', 'assembly': 'hg19', 'ID': 'chr8_gl000196_random'}
##contig={'length': '37175', 'assembly': 'hg19', 'ID': 'chr8_gl000197_random'}
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##contig={'length': '169874', 'assembly': 'hg19', 'ID': 'chr9_gl000199_random'}
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##contig={'length': '41934', 'assembly': 'hg19', 'ID': 'chrUn_gl000236'}
##contig={'length': '45867', 'assembly': 'hg19', 'ID': 'chrUn_gl000237'}
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##contig={'length': '33824', 'assembly': 'hg19', 'ID': 'chrUn_gl000239'}
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##contig={'length': '42152', 'assembly': 'hg19', 'ID': 'chrUn_gl000241'}
##contig={'length': '43523', 'assembly': 'hg19', 'ID': 'chrUn_gl000242'}
##contig={'length': '43341', 'assembly': 'hg19', 'ID': 'chrUn_gl000243'}
##contig={'length': '39929', 'assembly': 'hg19', 'ID': 'chrUn_gl000244'}
##contig={'length': '36651', 'assembly': 'hg19', 'ID': 'chrUn_gl000245'}
##contig={'length': '38154', 'assembly': 'hg19', 'ID': 'chrUn_gl000246'}
##contig={'length': '36422', 'assembly': 'hg19', 'ID': 'chrUn_gl000247'}
##contig={'length': '39786', 'assembly': 'hg19', 'ID': 'chrUn_gl000248'}
##contig={'length': '38502', 'assembly': 'hg19', 'ID': 'chrUn_gl000249'}
##contig={'length': '155270560', 'assembly': 'hg19', 'ID': 'chrX'}
##contig={'length': '59373566', 'assembly': 'hg19', 'ID': 'chrY'}
##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA19239
chr1	65312657	.	G	.	.	.	.	GT	./.

ok
test_vcf_4_0 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1_bnd (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2, REF=A, ALT=[T])
Call(sample=Germline, GT=0|1, HAP=[35, 46], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1, HAP=[35, 46], MQ=['0', '0'])
Record(CHROM=1, POS=2, REF=T, ALT=[])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=1, POS=3, REF=A, ALT=[])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=2, POS=1, REF=G, ALT=[T])
Call(sample=Germline, GT=1|0, HAP=[17, 23], MQ=['0', '40'])
Call(sample=Tumor, GT=1|0, HAP=[17, 23], MQ=['0', '0'])
Record(CHROM=2, POS=2, REF=G, ALT=[])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=3, REF=G, ALT=[])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=4, REF=G, ALT=[])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|0|1, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '0', '40'], BHAP=['17>17', '23>23', '24>23'])
Record(CHROM=2, POS=6, REF=T, ALT=[])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1|0, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '40', '0'], BHAP=['17>17', '23>24', '24>24'])
Record(CHROM=2, POS=6, REF=T, ALT=[A])
Call(sample=Germline, GT=0|1, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '0', '0'])
Record(CHROM=2, POS=8, REF=T, ALT=[A])
Call(sample=Germline, GT=0|0, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '0'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '40', '40'])
ok
test_vcf_4_1_sv (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2827693, REF=CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA, ALT=[C])
Call(sample=NA00001, GT=1/1, GQ=13.9)
Record(CHROM=2, POS=321682, REF=T, ALT=[])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=2, POS=14477084, REF=C, ALT=[])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=3, POS=9425916, REF=C, ALT=[])
Call(sample=NA00001, GT=1/1, GQ=15.0)
Record(CHROM=3, POS=12665100, REF=A, ALT=[])
Call(sample=NA00001, GT=None, CN=3, GQ=0.0, CNQ=16.2)
Record(CHROM=4, POS=18665128, REF=T, ALT=[])
Call(sample=NA00001, GT=None, CN=5, GQ=0.0, CNQ=8.3)
ok

----------------------------------------------------------------------
Ran 45 tests in 8.240s

OK
py27 sdist-reinst: /Users/marca/dev/git-repos/PyVCF/.tox/dist/PyVCF-0.5.0-pre.zip
py27 runtests: commands[0]
running test
running build_py
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
running egg_info
writing requirements to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/requires.txt
writing /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/PKG-INFO
writing top-level names to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/top_level.txt
writing dependency_links to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/dependency_links.txt
writing entry points to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/entry_points.txt
reading manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
writing manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
running build_ext
/Users/marca/dev/git-repos/PyVCF/.tox/py27/lib/python2.7/site-packages/distribute-0.6.27-py2.7.egg/setuptools/command/test.py:115: UserWarning: Module argparse was already imported from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.pyc, but /Users/marca/dev/git-repos/PyVCF/.tox/py27/lib/python2.7/site-packages is being added to sys.path
add_activation_listener(lambda dist: dist.activate())
vcf ()
Doctest: vcf ... ok
testCalls (vcf.test.test_vcf.TestGatkOutput) ... ok
testFormats (vcf.test.test_vcf.TestGatkOutput) ... ok
testInfos (vcf.test.test_vcf.TestGatkOutput) ... ok
testSamples (vcf.test.test_vcf.TestGatkOutput) ... ok
testCalls (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testFormats (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testInfos (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestFreebayesOutput) ... ['BLANK', 'NA12878', 'NA12891', 'NA12892', 'NA19238', 'NA19239', 'NA19240']
ok
testSamples (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestSamtoolsOutput) ... ok
testWrite (vcf.test.test_vcf.TestWriter) ... ok
testFetchRange (vcf.test.test_vcf.TestTabix) ... ok
testFetchSite (vcf.test.test_vcf.TestTabix) ... ok
testOpenFilehandle (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilehandleGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilename (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilenameGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testApplyFilter (vcf.test.test_vcf.TestFilter) ... ok
testApplyMultipleFilters (vcf.test.test_vcf.TestFilter) ... ok
testParse (vcf.test.test_vcf.Test1kg) ... ok
test_issue_49 (vcf.test.test_vcf.Test1kg)
docstring for test_issue_49 ... ok
test_aaf (vcf.test.test_vcf.TestRecord) ... ok
test_call_rate (vcf.test.test_vcf.TestRecord) ... ok
test_is_deletion (vcf.test.test_vcf.TestRecord) ... ok
test_is_indel (vcf.test.test_vcf.TestRecord) ... ok
test_is_snp (vcf.test.test_vcf.TestRecord) ... Record(CHROM=20, POS=14370, REF=G, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[51, 51], DP=1, GQ=48)
Call(sample=NA00002, GT=1|0, HQ=[51, 51], DP=8, GQ=48)
Call(sample=NA00003, GT=1/1, HQ=[None, None], DP=5, GQ=43)
Record(CHROM=20, POS=17330, REF=T, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[58, 50], DP=3, GQ=49)
Call(sample=NA00002, GT=0|1, HQ=[65, 3], DP=5, GQ=3)
Call(sample=NA00003, GT=0/0, HQ=None, DP=3, GQ=41)
Record(CHROM=20, POS=1110696, REF=A, ALT=[G, T])
Call(sample=NA00001, GT=1|2, HQ=[23, 27], DP=6, GQ=21)
Call(sample=NA00002, GT=2|1, HQ=[18, 2], DP=0, GQ=2)
Call(sample=NA00003, GT=2/2, HQ=None, DP=4, GQ=35)
Record(CHROM=20, POS=1230237, REF=T, ALT=[None])
Call(sample=NA00001, GT=0|0, HQ=[56, 60], DP=7, GQ=54)
Call(sample=NA00002, GT=0|0, HQ=[51, 51], DP=4, GQ=48)
Call(sample=NA00003, GT=0/0, HQ=None, DP=2, GQ=61)
Record(CHROM=20, POS=1234567, REF=GTCT, ALT=[G, GTACT])
Call(sample=NA00001, GT=None, DP=4, GQ=35)
Call(sample=NA00002, GT=0/2, DP=2, GQ=17)
Call(sample=NA00003, GT=1/1, DP=3, GQ=40)
ok
test_is_sv (vcf.test.test_vcf.TestRecord) ... ok
test_is_sv_precise (vcf.test.test_vcf.TestRecord) ... ok
test_is_transition (vcf.test.test_vcf.TestRecord) ... ok
test_num_calls (vcf.test.test_vcf.TestRecord) ... ok
test_pi (vcf.test.test_vcf.TestRecord) ... ok
test_qual (vcf.test.test_vcf.TestRecord) ... ok
test_sv_end (vcf.test.test_vcf.TestRecord) ... ok
test_var_subtype (vcf.test.test_vcf.TestRecord) ... ok
test_var_type (vcf.test.test_vcf.TestRecord) ... ok
test_gt_bases (vcf.test.test_vcf.TestCall) ... ok
test_gt_types (vcf.test.test_vcf.TestCall) ... {'GT': '0|0', 'HQ': [51, 51], 'DP': 1, 'GQ': 48}
{'GT': '1|0', 'HQ': [51, 51], 'DP': 8, 'GQ': 48}
{'GT': '1/1', 'HQ': [None, None], 'DP': 5, 'GQ': 43}
{'GT': '0|0', 'HQ': [58, 50], 'DP': 3, 'GQ': 49}
{'GT': '0|1', 'HQ': [65, 3], 'DP': 5, 'GQ': 3}
{'GT': '0/0', 'HQ': None, 'DP': 3, 'GQ': 41}
{'GT': '1|2', 'HQ': [23, 27], 'DP': 6, 'GQ': 21}
{'GT': '2|1', 'HQ': [18, 2], 'DP': 0, 'GQ': 2}
{'GT': '2/2', 'HQ': None, 'DP': 4, 'GQ': 35}
{'GT': '0|0', 'HQ': [56, 60], 'DP': 7, 'GQ': 54}
{'GT': '0|0', 'HQ': [51, 51], 'DP': 4, 'GQ': 48}
{'GT': '0/0', 'HQ': None, 'DP': 2, 'GQ': 61}
{'GT': None, 'DP': 4, 'GQ': 35}
{'GT': '0/2', 'DP': 2, 'GQ': 17}
{'GT': '1/1', 'DP': 3, 'GQ': 40}
ok
test_phased (vcf.test.test_vcf.TestCall) ... ok
test_issue_16 (vcf.test.test_vcf.TestRegression) ... ok
test_null_mono (vcf.test.test_vcf.TestRegression) ... /Users/marca/dev/git-repos/PyVCF/build/lib/vcf/test/null_genotype_mono.vcf
##fileformat=VCFv4.1
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[np_control.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[tests/read_chr.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=info log_to_file=null help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig={'length': '249250621', 'assembly': 'hg19', 'ID': 'chr1'}
##contig={'length': '135534747', 'assembly': 'hg19', 'ID': 'chr10'}
##contig={'length': '135006516', 'assembly': 'hg19', 'ID': 'chr11'}
##contig={'length': '40103', 'assembly': 'hg19', 'ID': 'chr11_gl000202_random'}
##contig={'length': '133851895', 'assembly': 'hg19', 'ID': 'chr12'}
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##contig={'length': '37498', 'assembly': 'hg19', 'ID': 'chr17_gl000203_random'}
##contig={'length': '81310', 'assembly': 'hg19', 'ID': 'chr17_gl000204_random'}
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##contig={'length': '4262', 'assembly': 'hg19', 'ID': 'chr18_gl000207_random'}
##contig={'length': '59128983', 'assembly': 'hg19', 'ID': 'chr19'}
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##contig={'length': '159169', 'assembly': 'hg19', 'ID': 'chr19_gl000209_random'}
##contig={'length': '106433', 'assembly': 'hg19', 'ID': 'chr1_gl000191_random'}
##contig={'length': '547496', 'assembly': 'hg19', 'ID': 'chr1_gl000192_random'}
##contig={'length': '243199373', 'assembly': 'hg19', 'ID': 'chr2'}
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##contig={'length': '48129895', 'assembly': 'hg19', 'ID': 'chr21'}
##contig={'length': '27682', 'assembly': 'hg19', 'ID': 'chr21_gl000210_random'}
##contig={'length': '51304566', 'assembly': 'hg19', 'ID': 'chr22'}
##contig={'length': '198022430', 'assembly': 'hg19', 'ID': 'chr3'}
##contig={'length': '191154276', 'assembly': 'hg19', 'ID': 'chr4'}
##contig={'length': '590426', 'assembly': 'hg19', 'ID': 'chr4_ctg9_hap1'}
##contig={'length': '189789', 'assembly': 'hg19', 'ID': 'chr4_gl000193_random'}
##contig={'length': '191469', 'assembly': 'hg19', 'ID': 'chr4_gl000194_random'}
##contig={'length': '180915260', 'assembly': 'hg19', 'ID': 'chr5'}
##contig={'length': '171115067', 'assembly': 'hg19', 'ID': 'chr6'}
##contig={'length': '4622290', 'assembly': 'hg19', 'ID': 'chr6_apd_hap1'}
##contig={'length': '4795371', 'assembly': 'hg19', 'ID': 'chr6_cox_hap2'}
##contig={'length': '4610396', 'assembly': 'hg19', 'ID': 'chr6_dbb_hap3'}
##contig={'length': '4683263', 'assembly': 'hg19', 'ID': 'chr6_mann_hap4'}
##contig={'length': '4833398', 'assembly': 'hg19', 'ID': 'chr6_mcf_hap5'}
##contig={'length': '4611984', 'assembly': 'hg19', 'ID': 'chr6_qbl_hap6'}
##contig={'length': '4928567', 'assembly': 'hg19', 'ID': 'chr6_ssto_hap7'}
##contig={'length': '159138663', 'assembly': 'hg19', 'ID': 'chr7'}
##contig={'length': '182896', 'assembly': 'hg19', 'ID': 'chr7_gl000195_random'}
##contig={'length': '146364022', 'assembly': 'hg19', 'ID': 'chr8'}
##contig={'length': '38914', 'assembly': 'hg19', 'ID': 'chr8_gl000196_random'}
##contig={'length': '37175', 'assembly': 'hg19', 'ID': 'chr8_gl000197_random'}
##contig={'length': '141213431', 'assembly': 'hg19', 'ID': 'chr9'}
##contig={'length': '90085', 'assembly': 'hg19', 'ID': 'chr9_gl000198_random'}
##contig={'length': '169874', 'assembly': 'hg19', 'ID': 'chr9_gl000199_random'}
##contig={'length': '187035', 'assembly': 'hg19', 'ID': 'chr9_gl000200_random'}
##contig={'length': '36148', 'assembly': 'hg19', 'ID': 'chr9_gl000201_random'}
##contig={'length': '16571', 'assembly': 'hg19', 'ID': 'chrM'}
##contig={'length': '166566', 'assembly': 'hg19', 'ID': 'chrUn_gl000211'}
##contig={'length': '186858', 'assembly': 'hg19', 'ID': 'chrUn_gl000212'}
##contig={'length': '164239', 'assembly': 'hg19', 'ID': 'chrUn_gl000213'}
##contig={'length': '137718', 'assembly': 'hg19', 'ID': 'chrUn_gl000214'}
##contig={'length': '172545', 'assembly': 'hg19', 'ID': 'chrUn_gl000215'}
##contig={'length': '172294', 'assembly': 'hg19', 'ID': 'chrUn_gl000216'}
##contig={'length': '172149', 'assembly': 'hg19', 'ID': 'chrUn_gl000217'}
##contig={'length': '161147', 'assembly': 'hg19', 'ID': 'chrUn_gl000218'}
##contig={'length': '179198', 'assembly': 'hg19', 'ID': 'chrUn_gl000219'}
##contig={'length': '161802', 'assembly': 'hg19', 'ID': 'chrUn_gl000220'}
##contig={'length': '155397', 'assembly': 'hg19', 'ID': 'chrUn_gl000221'}
##contig={'length': '186861', 'assembly': 'hg19', 'ID': 'chrUn_gl000222'}
##contig={'length': '180455', 'assembly': 'hg19', 'ID': 'chrUn_gl000223'}
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##contig={'length': '211173', 'assembly': 'hg19', 'ID': 'chrUn_gl000225'}
##contig={'length': '15008', 'assembly': 'hg19', 'ID': 'chrUn_gl000226'}
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##contig={'length': '129120', 'assembly': 'hg19', 'ID': 'chrUn_gl000228'}
##contig={'length': '19913', 'assembly': 'hg19', 'ID': 'chrUn_gl000229'}
##contig={'length': '43691', 'assembly': 'hg19', 'ID': 'chrUn_gl000230'}
##contig={'length': '27386', 'assembly': 'hg19', 'ID': 'chrUn_gl000231'}
##contig={'length': '40652', 'assembly': 'hg19', 'ID': 'chrUn_gl000232'}
##contig={'length': '45941', 'assembly': 'hg19', 'ID': 'chrUn_gl000233'}
##contig={'length': '40531', 'assembly': 'hg19', 'ID': 'chrUn_gl000234'}
##contig={'length': '34474', 'assembly': 'hg19', 'ID': 'chrUn_gl000235'}
##contig={'length': '41934', 'assembly': 'hg19', 'ID': 'chrUn_gl000236'}
##contig={'length': '45867', 'assembly': 'hg19', 'ID': 'chrUn_gl000237'}
##contig={'length': '39939', 'assembly': 'hg19', 'ID': 'chrUn_gl000238'}
##contig={'length': '33824', 'assembly': 'hg19', 'ID': 'chrUn_gl000239'}
##contig={'length': '41933', 'assembly': 'hg19', 'ID': 'chrUn_gl000240'}
##contig={'length': '42152', 'assembly': 'hg19', 'ID': 'chrUn_gl000241'}
##contig={'length': '43523', 'assembly': 'hg19', 'ID': 'chrUn_gl000242'}
##contig={'length': '43341', 'assembly': 'hg19', 'ID': 'chrUn_gl000243'}
##contig={'length': '39929', 'assembly': 'hg19', 'ID': 'chrUn_gl000244'}
##contig={'length': '36651', 'assembly': 'hg19', 'ID': 'chrUn_gl000245'}
##contig={'length': '38154', 'assembly': 'hg19', 'ID': 'chrUn_gl000246'}
##contig={'length': '36422', 'assembly': 'hg19', 'ID': 'chrUn_gl000247'}
##contig={'length': '39786', 'assembly': 'hg19', 'ID': 'chrUn_gl000248'}
##contig={'length': '38502', 'assembly': 'hg19', 'ID': 'chrUn_gl000249'}
##contig={'length': '155270560', 'assembly': 'hg19', 'ID': 'chrX'}
##contig={'length': '59373566', 'assembly': 'hg19', 'ID': 'chrY'}
##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA19239
chr1	65312657	.	G	.	.	.	.	GT	./.

ok
test_vcf_4_0 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1_bnd (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2, REF=A, ALT=[T])
Call(sample=Germline, GT=0|1, HAP=[35, 46], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1, HAP=[35, 46], MQ=['0', '0'])
Record(CHROM=1, POS=2, REF=T, ALT=[])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=1, POS=3, REF=A, ALT=[])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=2, POS=1, REF=G, ALT=[T])
Call(sample=Germline, GT=1|0, HAP=[17, 23], MQ=['0', '40'])
Call(sample=Tumor, GT=1|0, HAP=[17, 23], MQ=['0', '0'])
Record(CHROM=2, POS=2, REF=G, ALT=[])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=3, REF=G, ALT=[])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=4, REF=G, ALT=[])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|0|1, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '0', '40'], BHAP=['17>17', '23>23', '24>23'])
Record(CHROM=2, POS=6, REF=T, ALT=[])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1|0, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '40', '0'], BHAP=['17>17', '23>24', '24>24'])
Record(CHROM=2, POS=6, REF=T, ALT=[A])
Call(sample=Germline, GT=0|1, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '0', '0'])
Record(CHROM=2, POS=8, REF=T, ALT=[A])
Call(sample=Germline, GT=0|0, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '0'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '40', '40'])
ok
test_vcf_4_1_sv (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2827693, REF=CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA, ALT=[C])
Call(sample=NA00001, GT=1/1, GQ=13.9)
Record(CHROM=2, POS=321682, REF=T, ALT=[])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=2, POS=14477084, REF=C, ALT=[])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=3, POS=9425916, REF=C, ALT=[])
Call(sample=NA00001, GT=1/1, GQ=15.0)
Record(CHROM=3, POS=12665100, REF=A, ALT=[])
Call(sample=NA00001, GT=None, CN=3, GQ=0.0, CNQ=16.2)
Record(CHROM=4, POS=18665128, REF=T, ALT=[])
Call(sample=NA00001, GT=None, CN=5, GQ=0.0, CNQ=8.3)
ok

----------------------------------------------------------------------
Ran 45 tests in 7.879s

OK
py32 sdist-reinst: /Users/marca/dev/git-repos/PyVCF/.tox/dist/PyVCF-0.5.0-pre.zip
py32 runtests: commands[0]
running test
running build_py
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
running egg_info
writing requirements to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/requires.txt
writing /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/PKG-INFO
writing top-level names to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/top_level.txt
writing dependency_links to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/dependency_links.txt
writing entry points to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/entry_points.txt
reading manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
writing manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
running build_ext
/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py:115: UserWarning: Module argparse was already imported from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/argparse.py, but /Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages is being added to sys.path
add_activation_listener(lambda dist: dist.activate())
Traceback (most recent call last):
File "setup.py", line 65, in
'': ['*.vcf', '*.gz', '*.tbi'],
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 917, in run_commands
self.run_command(cmd)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py", line 137, in run
self.with_project_on_sys_path(self.run_tests)
File "/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py", line 117, in with_project_on_sys_path
func()
File "/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py", line 146, in run_tests
testLoader = loader_class()
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/main.py", line 123, in __init__
self.parseArgs(argv)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/main.py", line 191, in parseArgs
self.createTests()
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/main.py", line 198, in createTests
self.module)
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/loader.py", line 132, in loadTestsFromNames
suites = [self.loadTestsFromName(name, module) for name in names]
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/loader.py", line 132, in
suites = [self.loadTestsFromName(name, module) for name in names]
File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/loader.py", line 91, in loadTestsFromName
module = __import__('.'.join(parts_copy))
File "/Users/marca/dev/git-repos/PyVCF/build/lib/vcf/__init__.py", line 166, in
from parser import Reader, Writer
ImportError: cannot import name Reader
ERROR: InvocationError: '/Users/marca/dev/git-repos/PyVCF/.tox/py32/bin/python setup.py test'
_________________________________________________________________________ summary __________________________________________________________________________
py26: commands succeeded
py27: commands succeeded
ERROR: py32: commands failed
```