def get_genotype_tsv_text(cls, pgx_analysis: PgxAnalysis, panel: Panel,
version: str) -> str:
gene_to_haplotype_calls = pgx_analysis.get_gene_to_haplotype_calls()
genes_in_analysis = set(gene_to_haplotype_calls.keys())
assert genes_in_analysis == panel.get_genes(), (
f"Gene lists inconsistent.\n"
f"From analysis={sorted(list(genes_in_analysis))}\n"
f"From panel={sorted(list(panel.get_genes()))}")
gene_to_drug_info = {}
for gene_info in panel.get_gene_infos():
sorted_drugs = sorted([drug for drug in gene_info.drugs],
key=lambda info:
(info.name, info.url_prescription_info))
gene_to_drug_info[gene_info.gene] = (cls.DRUG_SEPARATOR.join(
[drug.name for drug in sorted_drugs]),
cls.DRUG_SEPARATOR.join([
drug.url_prescription_info
for drug in sorted_drugs
]))
header = cls.TSV_SEPARATOR.join(cls.GENOTYPE_TSV_COLUMNS)
lines = [header]
for gene in sorted(gene_to_haplotype_calls.keys()):
if gene_to_haplotype_calls[gene]:
for haplotype_call in sorted(
gene_to_haplotype_calls[gene],
key=lambda call: call.haplotype_name):
lines.append(
cls.TSV_SEPARATOR.join([
gene,
haplotype_call.haplotype_name,
cls.__get_zygosity(haplotype_call),
panel.get_haplotype_function(
gene, haplotype_call.haplotype_name),
gene_to_drug_info[gene][0],
gene_to_drug_info[gene][1],
panel.get_id(),
version,
]))
else:
lines.append(
cls.TSV_SEPARATOR.join([
gene,
cls.UNRESOLVED_HAPLOTYPE_STRING,
cls.NOT_APPLICABLE_ZYGOSITY_STRING,
UNKNOWN_FUNCTION_STRING,
gene_to_drug_info[gene][0],
gene_to_drug_info[gene][1],
panel.get_id(),
version,
]))
text = "\n".join(lines) + "\n"
return text
def __assert_gene_in_panel(cls, gene: str, panel: Panel) -> None:
if gene not in panel.get_genes():
error_msg = f"Call for unknown gene:\ngene={gene}"
raise ValueError(error_msg)