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import pandas as pd
import bioframe
def test_fetch_chromsizes():
db = "hg38"
for provider in ["local", "ucsc"]:
chromsizes = bioframe.fetch_chromsizes(db, provider=provider)
assert isinstance(chromsizes, pd.Series)
assert chromsizes.name == "length"
assert len(chromsizes) == 25
chromsizes_df = bioframe.fetch_chromsizes(db, provider=provider, as_bed=True)
assert isinstance(chromsizes_df, pd.DataFrame)
assert list(chromsizes_df.columns) == ["chrom", "start", "end"]
assert len(chromsizes_df) == 25
# Check synonymous local assemblies
assert bioframe.fetch_chromsizes("hg38", provider="local").equals(
bioframe.fetch_chromsizes("GRCh38", provider="local")
)
def test_fetch_chromsizes_local_vs_ucsc():
for db in ["hg19", "hg38", "mm9", "mm10"]:
assert bioframe.fetch_chromsizes(db, provider="local").equals(
bioframe.fetch_chromsizes(db, provider="ucsc")
)
def test_fetch_centromeres():
for db in ["hg19", "hg38"]:
# Note: UCSC will usually have a different ordering of chromosomes
for provider in ["local", "ucsc"]:
centromeres = bioframe.fetch_centromeres(db, provider=provider)
assert isinstance(centromeres, pd.DataFrame)
assert list(centromeres.columns) == ["chrom", "start", "end", "mid"]
assert len(centromeres) == 24
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