1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
|
import pandas as pd
import pytest
from bioframe.io.assembly import GenomeAssembly, assemblies_available, assembly_info
def test_assemblies_available():
assemblies = assemblies_available()
assert isinstance(assemblies, pd.DataFrame)
for col in ["provider", "provider_build", "default_roles", "default_units"]:
assert col in assemblies.columns
def test_assembly_info():
hg38 = assembly_info("hg38")
assert isinstance(hg38, GenomeAssembly)
assert hg38.provider == "ucsc"
assert hg38.provider_build == "hg38"
assert isinstance(hg38.chromsizes, pd.Series)
assert isinstance(hg38.chromnames, list)
assert isinstance(hg38.alias_dict, dict)
assert isinstance(hg38.seqinfo, pd.DataFrame)
for col in ["name", "length", "aliases", "role", "unit"]:
assert col in hg38.seqinfo.columns
assert isinstance(hg38.viewframe, pd.DataFrame)
for col in ["chrom", "start", "end", "name"]:
assert col in hg38.viewframe.columns
hg38 = assembly_info("ucsc.hg38", roles=("assembled", "unlocalized"))
assert isinstance(hg38, GenomeAssembly)
with pytest.raises(ValueError):
assembly_info("ncbi.hg38") # provider-name mismatch
assert isinstance(hg38.cytobands, pd.DataFrame)
for col in ["chrom", "start", "end", "band", "stain"]:
assert col in hg38.cytobands.columns
sacCer3 = assembly_info("sacCer3")
assert sacCer3.cytobands is None
|
