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)