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import os
import pytest
from pyfaidx import Faidx, Fasta
path = os.path.dirname(__file__)
os.chdir(path)
ACCESSION_TO_GENE_NAME_DICT = {
'gi|563317589|dbj|AB821309.1|': 'FGFR2',
'gi|557361099|gb|KF435150.1|': 'MDM4',
'gi|543583796|ref|NR_104216.1|': 'BARD1',
# The rest are deliberately omitted
# KF435149.1, NR_104215.1, NR_104212.1, NM_001282545.1 ...
}
ACCESSION_TO_DUPLICATED_GENE_NAME_DICT = {
'gi|563317589|dbj|AB821309.1|': 'FGFR2',
'gi|557361099|gb|KF435150.1|': 'MDM4',
'gi|543583796|ref|NR_104216.1|': 'BARD1',
'gi|543583795|ref|NR_104215.1|': 'BARD1', # Duplicated gene names will trigger a warning
# The rest are deliberately omitted
# KF435149.1, NR_104212.1, NM_001282545.1 ...
}
def get_gene_name(accession):
'''Return the gene name if found in ACCESSION_TO_GENE_NAME_DICT else return the original accession.'''
return ACCESSION_TO_GENE_NAME_DICT.get(accession, accession)
def get_duplicated_gene_name(accession):
'''Return the gene name if found in ACCESSION_TO_GENE_NAME_DICT else return the original accession.'''
return ACCESSION_TO_DUPLICATED_GENE_NAME_DICT.get(accession, accession)
@pytest.fixture
def remove_index():
genes = Fasta('data/genes.fasta')
del genes # Support feature introduced in #111
yield
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_keys(remove_index):
genes = Fasta('data/genes.fasta', key_function=get_gene_name)
expect = ['BARD1', 'FGFR2', 'MDM4', 'gi|530364724|ref|XR_241079.1|', 'gi|530364725|ref|XR_241080.1|', 'gi|530364726|ref|XR_241081.1|', 'gi|530373235|ref|XM_005265507.1|', 'gi|530373237|ref|XM_005265508.1|', 'gi|530384534|ref|XM_005249642.1|', 'gi|530384536|ref|XM_005249643.1|', 'gi|530384538|ref|XM_005249644.1|', 'gi|530384540|ref|XM_005249645.1|', 'gi|543583738|ref|NM_001282548.1|', 'gi|543583740|ref|NM_001282549.1|', 'gi|543583785|ref|NM_000465.3|', 'gi|543583786|ref|NM_001282543.1|', 'gi|543583788|ref|NM_001282545.1|', 'gi|543583794|ref|NR_104212.1|', 'gi|543583795|ref|NR_104215.1|', 'gi|557361097|gb|KF435149.1|']
result = sorted(genes.keys())
assert result == expect
def test_key_function_by_dictionary_get_key(remove_index):
genes = Fasta('data/genes.fasta', key_function=get_gene_name)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'
result = genes['MDM4'][100-1:150]
assert str(result) == expect
def test_key_function_by_fetch(remove_index):
faidx = Faidx('data/genes.fasta', key_function=get_gene_name)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'
result = faidx.fetch('MDM4',
100, 150)
assert str(result) == expect
def test_duplicated_keys(remove_index):
with pytest.raises(ValueError):
genes = Fasta('data/genes.fasta', key_function=get_duplicated_gene_name)
def test_duplicated_keys_shortest(remove_index):
genes = Fasta('data/genes.fasta', key_function=get_duplicated_gene_name, duplicate_action="shortest")
expect = 4573
result = len(genes["BARD1"])
assert expect == result
def test_duplicated_keys_longest(remove_index):
genes = Fasta('data/genes.fasta', key_function=get_duplicated_gene_name, duplicate_action="longest")
expect = 5317
result = len(genes["BARD1"])
assert expect == result
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