def test_gapfill(self):
join = os.path.join
inDir = util.file.get_test_input_path()
in_scaffold = join(inDir, 'TestOrderAndOrient', 'expected.ebov.doublehit.fasta')
with util.file.tempfname(suffix='.filled.fasta') as filled:
assembly.gapfill_gap2seq(in_scaffold=in_scaffold,
in_bam=join(inDir, 'G5012.3.testreads.bam'), out_scaffold=filled, random_seed=23923937)
self.assertEqualContents(filled, join(inDir, 'TestGap2Seq', 'expected.ebov.doublehit.gapfill.fasta'))
def test_gapfill(self):
join = os.path.join
inDir = util.file.get_test_input_path()
in_scaffold = join(inDir, 'TestOrderAndOrient', 'expected.ebov.doublehit.fasta')
with util.file.tempfname(suffix='.filled.fasta') as filled:
assembly.gapfill_gap2seq(in_scaffold=in_scaffold,
in_bam=join(inDir, 'G5012.3.testreads.bam'),
out_scaffold=filled, random_seed=23923937, threads=1)
shutil.copyfile(filled, '/tmp/filled.fasta')
self.assertEqualContents(filled, join(inDir, 'TestGap2Seq', 'expected.ebov.doublehit.gapfill.fasta'))