def load_config(genome_config, section_id):
genome = Genome(section_id)
genome.genomic_sequence_filename = genome_config.chr_all_file
for section_id, gene_models_config in \
genome_config.gene_models.items():
gene_models = Genome.GeneModelsConfig(
section_id,
gene_models_config.file,
gene_models_config.fileformat,
None,
)
genome._gene_models[gene_models.id] = gene_models
assert genome_config.default_gene_models in genome._gene_models
genome.default_gene_models_id = genome_config.default_gene_models
genome.default_gene_models_filename = \
genome._gene_models[genome.default_gene_models_id].file
if genome_config.pars:
assert genome_config.pars.X is not None
regions_x = [
Region.from_str(region) for region in genome_config.pars.X
]
chrom_x = regions_x[0].chrom
regions_y = [
Region.from_str(region) for region in genome_config.pars.Y
]
chrom_y = regions_y[0].chrom
genome.pars = {chrom_x: regions_x, chrom_y: regions_y}
return genome
def test_collapse_no_chrom_simple(regions, expected):
regions = [Region.from_str(r) for r in regions.split(",")]
result = collapse_no_chrom(regions)
assert len(result) == len(expected)
for res, exp in zip(result, expected):
assert res == exp
def reset_regions(self, regions):
super(DenovoLoader, self).reset_regions(regions)
result = []
for r in self.regions:
if r is None:
result.append(r)
else:
result.append(Region.from_str(r))
self.regions = result
logger.debug(f"denovo reset regions: {self.regions}")
def reset_regions(self, regions):
super(CNVLoader, self).reset_regions(regions)
result = []
for r in self.regions:
if r is None:
result.append(r)
else:
result.append(Region.from_str(r))
self.regions = result
print("CNV reset regions:", self.regions)
def test_parse_regions(region, expected):
result = Region.from_str(region)
# assert result is not None
assert result == expected