def test_make_polished_assembly_report_io(self):
"""
IOError if fasta does not exist
"""
with self.assertRaises(IOError):
make_polished_assembly_report(
'foo', 'bar', 'baz', self._output_dir)
def test_make_polished_assembly_report_io(self):
"""
IOError if fasta does not exist
"""
with self.assertRaises(IOError):
make_polished_assembly_report(
'foo', 'bar', 'baz', self._output_dir)
def test_make_polished_assembly_report(self):
"""
Test the attributes of the report
"""
make_polished_assembly_report('rpt.json', self.GFF, self.FASTQ, self._output_dir)
# deserialize report
s = None
with open(op.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
self.report = dict_to_report(s)
self._test_attribute("polished_contigs")
self._test_attribute("max_contig_length")
self._test_attribute("n_50_contig_length")
self._test_attribute("sum_contig_lengths")
def test_make_polished_assembly_report(self):
"""
Test the attributes of the report
"""
make_polished_assembly_report(
'rpt.json', self.GFF, self.FASTQ, self._output_dir)
# deserialize report
s = None
with open(op.join(self._output_dir, 'rpt.json'), 'r') as f:
s = json.load(f)
self.report = dict_to_report(s)
self._test_attribute("polished_contigs")
self._test_attribute("max_contig_length")
self._test_attribute("n_50_contig_length")
self._test_attribute("sum_contig_lengths")
def _create_polished_assembly_report(self):
"""
Creates and returns a Polished Assembly report
"""
from pbreports.report.polished_assembly import make_polished_assembly_report
datadir = os.path.join(ROOT_DATA_DIR, 'polished_assembly')
log.info(
'Creating Polished Assembly report using datadir {d}'.format(d=datadir))
gff = os.path.join(
ROOT_DATA_DIR, 'polished_assembly', 'alignment_summary.gff')
fastq = os.path.join(
ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fastq')
make_polished_assembly_report('polished_assembly.json', gff, fastq, self._output_dir)
return self._deserialize_report(os.path.join(self._output_dir, 'polished_assembly.json'))
def _create_polished_assembly_report(self):
"""
Creates and returns a Polished Assembly report
"""
from pbreports.report.polished_assembly import make_polished_assembly_report
datadir = os.path.join(ROOT_DATA_DIR, 'polished_assembly')
log.info('Creating Polished Assembly report using datadir {d}'.format(
d=datadir))
gff = os.path.join(ROOT_DATA_DIR, 'polished_assembly',
'alignment_summary.gff')
fastq = os.path.join(ROOT_DATA_DIR, 'polished_assembly',
'polished_assembly.fastq')
make_polished_assembly_report('polished_assembly.json', gff, fastq,
self._output_dir)
return self._deserialize_report(
os.path.join(self._output_dir, 'polished_assembly.json'))
def run_report(args):
return make_polished_assembly_report(args.report, args.gff, args.fastq, args.output)
