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import os
import tempfile
import pandas as pd
import pytest
import bioframe
def test_involution():
with tempfile.TemporaryDirectory() as directory:
for schema in ['narrowPeak', 'bed12']:
bf = bioframe.read_table(f'tests/test_data/{schema}.bed',
schema=schema)
fname = os.path.join(directory, f'{schema}.bed')
bioframe.to_bed(bf, fname)
involution = bioframe.read_table(fname, schema=schema)
pd.testing.assert_frame_equal(bf, involution)
def test_chrom_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'chrom'] = 'value with space'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'chrom'] = '' # must be non empty
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'chrom'] = 'a'*300 # must be shorter than 256
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_end_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'end'] = 10 # end must be after start
bf.loc[0, 'start'] = 11
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_name_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'name'] = '' # must not be empty
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'name'] = 'a'*300 # must be less than 255 char
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_score_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
# negative value is enforced by the normal types
bf.loc[0, 'score'] = 1001
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'), strict_score=True)
bf['score'] = '.' # enforced to be a number by the types
with pytest.raises(TypeError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_strand_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'strand'] = '*'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_thick_validators():
with tempfile.TemporaryDirectory() as directory:
for direction in ['Start', 'End']:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'start'] = 100
bf.loc[0, 'end'] = 1000
bf.loc[0, f'thick{direction}'] = 1001
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, f'thick{direction}'] = 99
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_itemRgb_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf["itemRgb"] = bf["itemRgb"].astype(str)
bf.loc[0, 'itemRgb'] = 'a,12,13' # must be integers
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'itemRgb'] = '12,13' # must be 1 or 3 integers
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'itemRgb'] = '12,13,14,15' # must be 1 or 3 integers
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'itemRgb'] = '12,13,300' # must be between 0 and 255
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'itemRgb'] = '300' # must be between 0 and 255
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_blockCount_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'blockCount'] = 0
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_blockSizes_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'blockCount'] = 2
bf.loc[0, 'blockSizes'] = '2,a,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'blockCount'] = 2
bf.loc[0, 'blockSizes'] = '2,2,2,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
def test_blockStarts_validators():
with tempfile.TemporaryDirectory() as directory:
bf = bioframe.read_table('tests/test_data/bed12.bed', schema='bed12')
bf.loc[0, 'blockCount'] = 2
bf.loc[0, 'blockSizes'] = '2,4,'
bf.loc[0, 'blockStarts'] = '0,a,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
bf.loc[0, 'blockCount'] = 2
bf.loc[0, 'blockSizes'] = '1,1,'
bf.loc[0, 'blockStarts'] = '0,2,5,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
# ends after end
bf.loc[0, 'start'] = 1
bf.loc[0, 'end'] = 10
bf.loc[0, 'blockCount'] = 1
bf.loc[0, 'blockSizes'] = '100,'
bf.loc[0, 'blockStarts'] = '0,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
# ends before end
bf.loc[0, 'start'] = 1
bf.loc[0, 'end'] = 10
bf.loc[0, 'blockCount'] = 1
bf.loc[0, 'blockSizes'] = '1,'
bf.loc[0, 'blockStarts'] = '0,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
# overlap
bf.loc[0, 'start'] = 1
bf.loc[0, 'end'] = 10
bf.loc[0, 'blockCount'] = 2
bf.loc[0, 'blockSizes'] = '5,5,'
bf.loc[0, 'blockStarts'] = '0,1,'
with pytest.raises(ValueError):
bioframe.to_bed(bf, os.path.join(directory, 'foo.bed'))
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