def main():
"""Main for imfusion-ctg."""
logger = logging.getLogger()
args = parse_args()
# Read insertions and filter for depth.
insertions = list(Insertion.from_csv(args.insertions, sep='\t'))
if args.min_depth is not None:
insertions = [
ins for ins in insertions if ins.support >= args.min_depth
]
# Identify CTGs.
logger.info('Testing for CTGs')
if args.window is not None:
logger.info('- Using window (%d, %d)', *args.window)
reference = Reference(args.reference)
ctgs = test_ctgs(insertions,
reference=reference,
gene_ids=args.gene_ids,
chromosomes=args.chromosomes,
pattern=args.pattern,
window=args.window)
# Filter using given threshold.
if args.threshold is not None:
ctgs = ctgs.query('q_value <= {}'.format(args.threshold))
# If expression is given, test for differential expression.
if args.expression is not None:
logger.info('Testing for differential expression')
# Perform DE tests.
exon_counts = read_exon_counts(args.expression)
de_results = test_de(insertions, exon_counts, gene_ids=ctgs['gene_id'])
# Combine with CTG result.
de_results = de_results.rename(
columns={
'direction': 'de_direction',
'p_value': 'de_pvalue',
'test_type': 'de_test'
})
col_order = (list(ctgs.columns) +
['de_test', 'de_direction', 'de_pvalue'])
ctgs = pd.merge(ctgs, de_results, on='gene_id', how='left')[col_order]
if args.de_threshold is not None:
# Filter for non-significant genes, keeping nans.
ctgs = ctgs.loc[~(ctgs['de_pvalue'] > args.de_threshold)]
# Write outputs.
logger.info('Writing outputs')
ctgs.to_csv(str(args.output), sep='\t', index=False)
def main():
"""Main for imfusion-ctg."""
logger = logging.getLogger()
args = parse_args()
# Read insertions and filter for depth.
insertions = list(Insertion.from_csv(args.insertions, sep='\t'))
if args.min_depth is not None:
insertions = [
ins for ins in insertions if ins.support >= args.min_depth
]
# Identify CTGs.
logger.info('Testing for CTGs')
if args.window is not None:
logger.info('- Using window (%d, %d)', *args.window)
reference = Reference(args.reference)
ctgs = test_ctgs(
insertions,
reference=reference,
gene_ids=args.gene_ids,
chromosomes=args.chromosomes,
pattern=args.pattern,
window=args.window)
# Filter using given threshold.
if args.threshold is not None:
ctgs = ctgs.query('q_value <= {}'.format(args.threshold))
# If expression is given, test for differential expression.
if args.expression is not None:
logger.info('Testing for differential expression')
# Perform DE tests.
exon_counts = read_exon_counts(args.expression)
de_results = test_de(insertions, exon_counts, gene_ids=ctgs['gene_id'])
# Combine with CTG result.
de_results = de_results.rename(columns={
'direction': 'de_direction',
'p_value': 'de_pvalue',
'test_type': 'de_test'
})
col_order = (
list(ctgs.columns) + ['de_test', 'de_direction', 'de_pvalue'])
ctgs = pd.merge(ctgs, de_results, on='gene_id', how='left')[col_order]
if args.de_threshold is not None:
# Filter for non-significant genes, keeping nans.
ctgs = ctgs.loc[~(ctgs['de_pvalue'] > args.de_threshold)]
# Write outputs.
logger.info('Writing outputs')
ctgs.to_csv(str(args.output), sep='\t', index=False)
def test_example_with_chromosomes(self, ctg_insertions, ctg_reference):
"""Tests subsetting for specific chromosomes."""
# Do CTG test.
result = ctg.test_ctgs(
ctg_insertions, ctg_reference, chromosomes=['1'], per_sample=True)
assert len(result) == 2
assert set(result['gene_id']) == {'gene_a', 'gene_b'}
def test_empty(self, ctg_reference):
"""Test example without insertions."""
result = ctg.test_ctgs(
[], ctg_reference, window=(4, 0), per_sample=False)
assert len(result) == 0
assert list(result.columns) == [
'gene_id', 'p_value', 'q_value', 'gene_name', 'n_samples'
]
def test_example_with_chromosomes(self, ctg_insertions, ctg_reference):
"""Tests subsetting for specific chromosomes."""
# Do CTG test.
result = ctg.test_ctgs(ctg_insertions,
ctg_reference,
chromosomes=['1'],
per_sample=True)
assert len(result) == 2
assert set(result['gene_id']) == {'gene_a', 'gene_b'}
def test_example_with_window(self, ctg_insertions, ctg_reference):
"""Tests applying a gene window."""
# TODO: check the generated windows.
# Do CTG test.
result = ctg.test_ctgs(
ctg_insertions, ctg_reference, window=(4, 0), per_sample=False)
result = result.set_index('gene_id')
# Check result.
assert result.loc['gene_a', 'p_value'] < 0.05
def test_example_with_collapse(self, ctg_insertions, ctg_reference):
"""Tests if gene_a is no longer significant after collapsing."""
# Do CTG test.
result = ctg.test_ctgs(ctg_insertions, ctg_reference, per_sample=True)
result = result.set_index('gene_id')
# Check results.
assert len(result) == 3
assert result.loc['gene_a', 'p_value'] > 0.05
assert result.loc['gene_b', 'p_value'] > 0.05
assert result.loc['gene_c', 'p_value'] > 0.05
def test_empty(self, ctg_reference):
"""Test example without insertions."""
result = ctg.test_ctgs([],
ctg_reference,
window=(4, 0),
per_sample=False)
assert len(result) == 0
assert list(result.columns) == [
'gene_id', 'p_value', 'q_value', 'gene_name', 'n_samples'
]
def test_example_with_collapse(self, ctg_insertions, ctg_reference):
"""Tests if gene_a is no longer significant after collapsing."""
# Do CTG test.
result = ctg.test_ctgs(ctg_insertions, ctg_reference, per_sample=True)
result = result.set_index('gene_id')
# Check results.
assert len(result) == 3
assert result.loc['gene_a', 'p_value'] > 0.05
assert result.loc['gene_b', 'p_value'] > 0.05
assert result.loc['gene_c', 'p_value'] > 0.05
def test_example(self, ctg_insertions, ctg_reference):
"""Test example with three genes."""
# TODO: P-values seem higher than in previous tests. Check why.
# Do CTG test.
result = ctg.test_ctgs(ctg_insertions, ctg_reference, per_sample=False)
result = result.set_index('gene_id')
# Check results.
assert len(result) == 3
assert result.loc['gene_a', 'p_value'] < 0.05
assert result.loc['gene_b', 'p_value'] > 0.05
assert result.loc['gene_c', 'p_value'] > 0.05
def test_example_with_window(self, ctg_insertions, ctg_reference):
"""Tests applying a gene window."""
# TODO: check the generated windows.
# Do CTG test.
result = ctg.test_ctgs(ctg_insertions,
ctg_reference,
window=(4, 0),
per_sample=False)
result = result.set_index('gene_id')
# Check result.
assert result.loc['gene_a', 'p_value'] < 0.05
def test_example(self, ctg_insertions, ctg_reference):
"""Test example with three genes."""
# TODO: P-values seem higher than in previous tests. Check why.
# Do CTG test.
result = ctg.test_ctgs(ctg_insertions, ctg_reference, per_sample=False)
result = result.set_index('gene_id')
# Check results.
assert len(result) == 3
assert result.loc['gene_a', 'p_value'] < 0.05
assert result.loc['gene_b', 'p_value'] > 0.05
assert result.loc['gene_c', 'p_value'] > 0.05