def test_bowtie(self):
nesoni.Analyse_sample(
output_dir=output / 'test-analyse',
reference=output / 'reference',
pairs=[[data / 'reads_1.txt.gz', data / 'reads_2.txt.gz']],
align=nesoni.Bowtie(),
).run()
def test_check_names(self):
with self.assertRaises(AssertionError):
nesoni.Analyse_sample(
output_dir=output / 'test-analyse',
reference=output / 'reference',
clip=None,
pairs=[[data / 'reads_1.txt.gz', data / 'reads_2.txt.gz'],
[data / 'reads_1.txt.gz',
data / 'reads_2.txt.gz']]).run()
with self.assertRaises(AssertionError):
nesoni.Analyse_sample(
output_dir=output / 'test-analyse',
reference=output / 'reference',
clip=None,
reads=[data / 'reads_1.txt.gz',
data / 'reads_1.txt.gz']).run()
with self.assertRaises(AssertionError):
nesoni.Analyse_sample(output_dir=output / 'test-analyse',
reference=output / 'reference',
clip=None,
interleaved=[data / 'reads_1.txt.gz']).run()
def test_analyse(self):
nesoni.Analyse_sample(
output_dir=output / 'test-analyse',
reference=output / 'reference',
pairs=[[data / 'reads_1.txt.gz', data / 'reads_2.txt.gz']]).run()
nesoni.Nway(output=output / 'test-nway.txt',
working_dirs=[output / 'test-analyse']).run()
nesoni.Core(
output_dir=output / 'test-core',
working_dirs=[output / 'test-analyse'],
what='core',
).run()
nesoni.Core(
output_dir=output / 'test-unique',
working_dirs=[output / 'test-analyse'],
what='unique',
).run()
def run(self):
work = self.get_workspace()
with nesoni.Stage() as stage:
for accession in self.genbanks:
Fetch_genbank(
work / 'genbank',
accession,
self.email,
).process_make(stage)
for accession in self.accessions:
Fetch_sra(work / 'sra', accession).process_make(stage)
nesoni.Make_reference(
output_dir=work / 'TW20',
filenames=[
work / ('genbank', accession + '.gbk')
for accession in self.genbanks
],
genome=True,
bowtie=True,
ls=True,
snpeff=True,
).make()
analyser = nesoni.Analyse_samples
analyser(work / 'analysis',
work / 'TW20',
samples=[
nesoni.Analyse_sample(
accession,
pairs=[[
work / ('sra', accession + '_1.fastq.bz2'),
work / ('sra', accession + '_2.fastq.bz2')
]]) for accession in self.accessions
]).make()
variants)
def rand_seq(n):
return ''.join(random.choice('ACGT') for i in xrange(n))
@config.Positional('ref', 'Reference sequence\neg AAG')
@config.Main_section(
'variants', 'Variants, each with a number of reads, eg ACGx10 ATGx5. '
'The first variant given is treated as the correct variant.')
@config.Configurable_section(
'analysis',
'Options for "nesoni analyse-sample:"',
presets=[
('shrimp', lambda obj: nesoni.Analyse_sample(clip=None),
'Do analysis using SHRiMP'),
('bowtie',
lambda obj: nesoni.Analyse_sample(clip=None, align=bowtie.Bowtie()),
'Do analysis using Bowtie'),
])
@config.Configurable_section('freebayes',
'Options for "nesoni freebayes:"',
presets=[
('freebayes', lambda obj: Freebayes(), ''),
])
@config.Configurable_section('vcf_filter',
'Options for "nesoni vcf-filter:"',
presets=[
('vcf-filter', lambda obj: Vcf_filter(), ''),
])