def test_make_topvariants_report_inputs(self):
"""
in inputs
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
# test how_many
with self.assertRaises(ValueError):
make_topvariants_report(gff, ref, 'foo.json', None, 10, self._output_dir)
# test batch size
with self.assertRaises(ValueError):
make_topvariants_report(gff, ref, 'foo.json', 1, None, self._output_dir)
def test_make_topvariants_report_inputs(self):
"""
in inputs
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
# test how_many
with self.assertRaises(ValueError):
make_topvariants_report(gff, ref, 'foo.json', None, 10,
self._output_dir)
# test batch size
with self.assertRaises(ValueError):
make_topvariants_report(gff, ref, 'foo.json', 1, None,
self._output_dir)
def test_make_minor_topvariants_report(self):
"""
Call the main report generation method with minor kwarg==True. Deserialize report, check content.
"""
ref = self.REFERENCE
gff = self.RARE_VARIANTS_GFF
make_topvariants_report(gff, ref, 100, 10000, 'rpt.json', self._output_dir, is_minor_variants_rpt=True)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
self.assertEqual('Frequency', report.tables[0].columns[6].header)
def test_make_minor_topvariants_report(self):
"""
Call the main report generation method with minor kwarg==True. Deserialize report, check content.
"""
ref = self.REFERENCE
gff = self.RARE_VARIANTS_GFF
make_topvariants_report(
gff, ref, 100, 10000, 'rpt.json', self._output_dir, is_minor_variants_rpt=True)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
def test_make_topvariants_report(self):
"""
Call the main report generation method. Deserialize report, check content.
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
make_topvariants_report(gff, ref, 100, 10000,
'rpt.json', self._output_dir)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
def test_make_minor_topvariants_report(self):
"""
Call the main report generation method with minor kwarg==True. Deserialize report, check content.
"""
ref = self.REFERENCE
gff = self.RARE_VARIANTS_GFF
make_topvariants_report(
gff, ref, 100, 10000, 'rpt.json', self._output_dir, is_minor_variants_rpt=True)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
validate_report_complete(self, report)
def test_make_topvariants_report(self):
"""
Call the main report generation method. Deserialize report, check content.
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
make_topvariants_report(gff, ref, 100, 10000, 'rpt.json',
self._output_dir)
# deserialize report
s = None
with open(os.path.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
report = dict_to_report(s)
validate_report_complete(self, report)
def _create_top_variants_report(self):
"""
Creates and returns a Top Variants report.
"""
from pbreports.report.top_variants import make_topvariants_report
datadir = os.path.join(ROOT_DATA_DIR, 'topvariants')
log.info(
'Creating top variants report using datadir {d}'.format(d=datadir))
ref = os.path.join(datadir, 'ecoliK12_pbi_March2013')
gff = os.path.join(datadir, 'variants.gff.gz')
how_many = 100
batch_sort_size = 10000
report = 'topvariants.json'
output_json = os.path.join(self._output_dir, report)
make_topvariants_report(gff, ref, how_many, batch_sort_size, report,
self._output_dir)
return self._deserialize_report(output_json)
def _create_top_variants_report(self):
"""
Creates and returns a Top Variants report.
"""
from pbreports.report.top_variants import make_topvariants_report
datadir = os.path.join(ROOT_DATA_DIR, 'topvariants')
log.info(
'Creating top variants report using datadir {d}'.format(d=datadir))
ref = os.path.join(datadir, 'ecoliK12_pbi_March2013')
gff = os.path.join(datadir, 'variants.gff.gz')
how_many = 100
batch_sort_size = 10000
report = 'topvariants.json'
output_json = os.path.join(self._output_dir, report)
make_topvariants_report(gff, ref, how_many, batch_sort_size, report,
self._output_dir)
return self._deserialize_report(output_json)
def test_make_topvariants_report_input_files(self):
"""
input gff and ref must be non-null and exist
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
# test gff
with self.assertRaises(PbReportError):
make_topvariants_report(None, ref, 'foo.json', 1, 10, self._output_dir)
with self.assertRaises(IOError):
make_topvariants_report('foo', ref, 'foo.json', 1, 10, self._output_dir)
# test ref
with self.assertRaises(PbReportError):
make_topvariants_report(gff, None, 'foo.json', 1, 10, self._output_dir)
with self.assertRaises(IOError):
make_topvariants_report(gff, 'foo', 'foo.json', 1, 10, self._output_dir)
def test_make_topvariants_report_input_files(self):
"""
input gff and ref must be non-null and exist
"""
ref = self.REFERENCE
gff = self.VARIANTS_GFF
# test gff
with self.assertRaises(PbReportError):
make_topvariants_report(None, ref, 'foo.json', 1, 10,
self._output_dir)
with self.assertRaises(IOError):
make_topvariants_report('foo', ref, 'foo.json', 1, 10,
self._output_dir)
# test ref
with self.assertRaises(PbReportError):
make_topvariants_report(gff, None, 'foo.json', 1, 10,
self._output_dir)
with self.assertRaises(IOError):
make_topvariants_report(gff, 'foo', 'foo.json', 1, 10,
self._output_dir)
def run_report(args):
return make_topvariants_report(args.gff, args.reference,
args.how_many, args.batch_sort_size, args.report, args.output, True)