def test_empty_file(self):
gff_tmp = tempfile.NamedTemporaryFile(suffix=".gff").name
with open(gff_tmp, "w") as f:
f.write("##gff-version 3\n")
f.write("##source ipdSummary\n")
f.write("##sequence-region lambda_NEB3011 1 48502")
gff_out = tempfile.NamedTemporaryFile(suffix=".gff").name
merge_gffs(self.files + [gff_tmp], gff_out)
rm_out(gff_out)
def test_empty_file(self):
gff_tmp = tempfile.NamedTemporaryFile(suffix=".gff").name
with open(gff_tmp, "w") as f:
f.write("##gff-version 3\n")
f.write("##source ipdSummary\n")
f.write("##sequence-region lambda_NEB3011 1 48502")
gff_out = tempfile.NamedTemporaryFile(suffix=".gff").name
merge_gffs(self.files + [gff_tmp], gff_out)
rm_out(gff_out)
def test_merge_gffs(self):
gff_out = "tmp_pbcore_merge.gff"
merge_gffs(self.files, gff_out)
n_rec = 0
for fn in self.files:
with GffReader(fn) as f:
n_rec += len([ rec for rec in f ])
with GffReader(gff_out) as f:
self.assertEqual(f.headers, [
"##gff-version 3",
"##source ipdSummary",
"##sequence-region lambda_NEB3011 1 48502",
])
n_rec_merged = len([ rec for rec in f ])
self.assertEqual(n_rec, n_rec_merged)
def test_merge_gffs(self):
gff_out = "tmp_pbcore_merge.gff"
merge_gffs(self.files, gff_out)
n_rec = 0
for fn in self.files:
with GffReader(fn) as f:
n_rec += len([rec for rec in f])
with GffReader(gff_out) as f:
assert f.headers == [
"##gff-version 3",
"##source ipdSummary",
"##sequence-region lambda_NEB3011 1 48502",
]
n_rec_merged = len([rec for rec in f])
assert n_rec == n_rec_merged
rm_out(gff_out)
def test_merge_gffs(self):
gff_out = "tmp_pbcore_merged.gff"
merge_gffs(self.files, gff_out)
with GffReader(gff_out) as f:
start = [ (rec.seqid, rec.start) for rec in f ]
self.assertEqual(start, self.sorted_start)
