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Merge pull request #116 from apriha/hotfix/updates-for-new-gene-resou…
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Updates for new gene resources
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@apriha
apriha authored Dec 4, 2024
2 parents ecafc80 + 6ae2305 commit 54d0219
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4 changes: 2 additions & 2 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -227,11 +227,11 @@ chromosomes are also output.
.. note:: Shared DNA is not computed on the X chromosome with the 1000 Genomes Project genetic
maps since the X chromosome is not included in these genetic maps.

In this example, there are 51,740 shared genes/transcripts on both chromosomes transcribed from 36 segments
In this example, there are 77,776 shared genes/transcripts on both chromosomes transcribed from 36 segments
of shared DNA:

>>> len(results['two_chrom_shared_genes'])
51740
77776
>>> len(results['two_chrom_shared_dna'])
36

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42 changes: 21 additions & 21 deletions tests/test_lineage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,8 @@ def _generate_test_cytoBand_hg19(self):
def _generate_test_gene_dfs(
self,
chrom="1",
len1=11421,
len2=12000,
len1=16267,
len2=18000,
txStart1=1000000,
txEnd1=2000000,
txStart2=111600000,
Expand Down Expand Up @@ -133,8 +133,8 @@ def run_find_shared_dna_test_X(self, f):
20.837792 + 180.837755,
20.837792 + 180.837755 + 0.347344,
),
len1=146,
len2=8243,
len1=278,
len2=11432,
txStart1=2400000,
txEnd1=2600000,
txStart2=150000000,
Expand All @@ -148,7 +148,7 @@ def run_find_shared_dna_test_1000G(self, f):
pos=(1, 43800001),
rate=(63.0402663602 / (43800001 / 1e6), 0),
map_cMs=(0.0, 63.0402663602),
len1=6096,
len1=8742,
)

def run_find_shared_dna_test(self, f, HapMap2=True, **kwargs):
Expand Down Expand Up @@ -388,8 +388,8 @@ def _test_find_shared_dna_two_chrom_shared(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 1
assert len(d["one_chrom_shared_genes"]) == 11421
assert len(d["two_chrom_shared_genes"]) == 11421
assert len(d["one_chrom_shared_genes"]) == 16267
assert len(d["two_chrom_shared_genes"]) == 16267
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
np.testing.assert_allclose(
Expand All @@ -416,8 +416,8 @@ def _test_find_shared_dna_two_chrom_shared_1000G(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 1
assert len(d["one_chrom_shared_genes"]) == 6096
assert len(d["two_chrom_shared_genes"]) == 6096
assert len(d["one_chrom_shared_genes"]) == 8742
assert len(d["two_chrom_shared_genes"]) == 8742
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
np.testing.assert_allclose(
Expand Down Expand Up @@ -447,8 +447,8 @@ def _test_find_shared_dna_two_chrom_shared_three_ind(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 1
assert len(d["one_chrom_shared_genes"]) == 11421
assert len(d["two_chrom_shared_genes"]) == 11421
assert len(d["one_chrom_shared_genes"]) == 16267
assert len(d["two_chrom_shared_genes"]) == 16267
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
np.testing.assert_allclose(
Expand All @@ -475,8 +475,8 @@ def _test_find_shared_dna_two_chrom_shared_no_output(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 1
assert len(d["one_chrom_shared_genes"]) == 11421
assert len(d["two_chrom_shared_genes"]) == 11421
assert len(d["one_chrom_shared_genes"]) == 16267
assert len(d["two_chrom_shared_genes"]) == 16267
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
np.testing.assert_allclose(
Expand Down Expand Up @@ -505,7 +505,7 @@ def _test_find_shared_dna_one_chrom_shared(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 0
assert len(d["one_chrom_shared_genes"]) == 11421
assert len(d["one_chrom_shared_genes"]) == 16267
assert len(d["two_chrom_shared_genes"]) == 0
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
Expand Down Expand Up @@ -535,7 +535,7 @@ def _test_find_shared_dna_one_chrom_shared_three_ind(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 0
assert len(d["one_chrom_shared_genes"]) == 11421
assert len(d["one_chrom_shared_genes"]) == 16267
assert len(d["two_chrom_shared_genes"]) == 0
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
Expand Down Expand Up @@ -574,8 +574,8 @@ def _test_find_shared_dna_X_chrom_two_individuals_male(self):

assert len(d["one_chrom_shared_dna"]) == 1 # PAR1, non-PAR, PAR2
assert len(d["two_chrom_shared_dna"]) == 1 # PAR1
assert len(d["one_chrom_shared_genes"]) == 8243
assert len(d["two_chrom_shared_genes"]) == 146
assert len(d["one_chrom_shared_genes"]) == 11432
assert len(d["two_chrom_shared_genes"]) == 278
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
np.testing.assert_allclose(
Expand Down Expand Up @@ -616,8 +616,8 @@ def _test_find_shared_dna_X_chrom_two_individuals_female(self):

assert len(d["one_chrom_shared_dna"]) == 1 # PAR1, non-PAR, PAR2
assert len(d["two_chrom_shared_dna"]) == 1 # PAR1, non-PAR, PAR2
assert len(d["one_chrom_shared_genes"]) == 8243
assert len(d["two_chrom_shared_genes"]) == 8243
assert len(d["one_chrom_shared_genes"]) == 11432
assert len(d["two_chrom_shared_genes"]) == 11432
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 0
np.testing.assert_allclose(
Expand Down Expand Up @@ -653,8 +653,8 @@ def _test_find_shared_dna_two_chrom_shared_discrepant_snps(self):

assert len(d["one_chrom_shared_dna"]) == 1
assert len(d["two_chrom_shared_dna"]) == 1
assert len(d["one_chrom_shared_genes"]) == 11421
assert len(d["two_chrom_shared_genes"]) == 11421
assert len(d["one_chrom_shared_genes"]) == 16267
assert len(d["two_chrom_shared_genes"]) == 16267
assert len(d["one_chrom_discrepant_snps"]) == 0
assert len(d["two_chrom_discrepant_snps"]) == 2
np.testing.assert_allclose(
Expand Down
12 changes: 6 additions & 6 deletions tests/test_resources.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,7 @@ def f():
assert len(cytoBand_hg19) == 862

def _generate_test_knownGene_hg19_resource(self):
s = "s\ts\ts\t0\t0\t0\t0\t0\ts\ts\ts\ts\n" * 254535
s = "s\ts\ts\t0\t0\t0\t0\t0\ts\ts\ts\ts\n" * 381974

mock = mock_open(read_data=gzip.compress(s.encode()))
with patch("urllib.request.urlopen", mock):
Expand All @@ -207,14 +207,14 @@ def f():
self.resource.get_knownGene_hg19() if self.downloads_enabled else f()
)

assert len(knownGene_hg19) == 254535
assert len(knownGene_hg19) == 381974

# get already loaded resource
knownGene_hg19 = self.resource.get_knownGene_hg19()
assert len(knownGene_hg19) == 254535
assert len(knownGene_hg19) == 381974

def _generate_test_kgXref_hg19_resource(self):
s = "s\ts\ts\ts\ts\ts\ts\ts\n" * 254491
s = "s\ts\ts\ts\ts\ts\ts\ts\n" * 381930

mock = mock_open(read_data=gzip.compress(s.encode()))
with patch("urllib.request.urlopen", mock):
Expand All @@ -228,11 +228,11 @@ def f():

kgXref_hg19 = self.resource.get_kgXref_hg19() if self.downloads_enabled else f()

assert len(kgXref_hg19) == 254491
assert len(kgXref_hg19) == 381930

# get already loaded resource
kgXref_hg19 = self.resource.get_kgXref_hg19()
assert len(kgXref_hg19) == 254491
assert len(kgXref_hg19) == 381930

def test_get_all_resources(self):
def f():
Expand Down

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