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Add gene name to report #202

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Add gene name to report #202

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add gene name to report xlsx and csv
timodonnell Jul 26, 2024
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timodonnell Jul 26, 2024
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timodonnell Jul 28, 2024
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6 changes: 4 additions & 2 deletions vaxrank/report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -426,6 +426,7 @@ def new_columns():
("pos", []),
("ref", []),
("alt", []),
("gene_name", []),
("variant_rank", []),
("peptide_rank", []),
("mutation_start", []),
Expand Down Expand Up @@ -512,7 +513,7 @@ def make_minimal_neoepitope_report(
worksheet.set_column('%s:%s' % ('G', 'G'), 30)
worksheet.set_column('%s:%s' % ('H', 'H'), 9)
worksheet.set_column('%s:%s' % ('I', 'I'), 18)
writer.save()
writer.close()
logger.info('Wrote XLSX neoepitope report file to %s', excel_report_path)


Expand Down Expand Up @@ -546,6 +547,7 @@ def make_csv_report(
columns["pos"].append(variant.original_start)
columns["ref"].append(variant.original_ref)
columns["alt"].append(variant.original_alt)
columns["gene_name"].append(vaccine_peptide.mutant_protein_fragment.gene_name)
columns["variant_rank"].append(i + 1)
columns["peptide_rank"].append(j + 1)
columns["amino_acids"].append(vaccine_peptide.mutant_protein_fragment.amino_acids)
Expand Down Expand Up @@ -596,5 +598,5 @@ def make_csv_report(
df.to_excel(writer, sheet_name=shortened_sheet_name, index=False)
resize_columns(writer.sheets[shortened_sheet_name], 'A', 'C')

writer.save()
writer.close()
logger.info('Wrote manufacturer XLSX file to %s', excel_report_path)