| import os |
| import pandas as pd |
| import re |
| import sys |
|
|
| def write_to_excel(output_filename, dfs_towrite, index = False, col_width=22): |
| with pd.ExcelWriter(output_filename) as writer: |
| for name, df in dfs_towrite.items(): |
| df.to_excel(writer, sheet_name = name, index = index) |
| num_col = len(df.columns) if index else len(df.columns)-1 |
| writer.sheets[name].set_column(0, num_col, col_width) |
| print("Write to", output_filename) |
|
|
| def read_model_excel(model_excel_filename, sheet_name): |
| if not os.path.isfile(model_excel_filename): |
| raise FileNotFoundError(f"Missing model excel file, expected at {model_excel_filename}") |
| if sheet_name not in pd.ExcelFile(model_excel_filename).sheet_names: |
| raise ValueError(f"{sheet_name} are expected to be in the parsed model excel file - {model_excel_filename}") |
| sheet_df = pd.read_excel(model_excel_filename, sheet_name=sheet_name) |
| sheet_df = sheet_df.fillna("") |
| return sheet_df |
|
|
| def read_mapping(mapping_filename): |
| if not os.path.isfile(mapping_filename): |
| raise FileNotFoundError(f"Missing mapping file, expected at {mapping_filename}") |
|
|
| mapping_df = pd.read_excel(mapping_filename) |
| mapping_df = mapping_df[mapping_df["has_mapping"] == True] |
|
|
| mapping_dict = dict(zip(mapping_df["model_tag"], mapping_df["gene_id"])) |
| return mapping_dict |
