file_process.py

'''
Functon: TSV file conversion to dataframe
Input: TSV file
Output: Dataframe

Author: Hansi Thewarapperuma
Date: 25/12/2022
'''

import pandas as pd

def tsv_to_df_filter_genes(user_tsv):
    try:
        # Read the TSV file into a DataFrame using pandas
        input_variants_df = pd.read_csv(user_tsv, sep='\t', encoding='latin1')

        # Read the virtual gene panel from the specified file
        with open('gene_panel_file.txt', 'r') as gene_file:
            # Split each line into cancer type and associated genes
            virtual_gene_panel = {line.split(': ')[0]: line.split(': ')[1].split() for line in gene_file}

        # Assuming gene names are in the column 'ANN[0].GENE', filter rows based on virtual gene panel
        gene_column_name = 'ANN[0].GENE'
        filtered_df = input_variants_df[input_variants_df[gene_column_name].isin([gene for genes in virtual_gene_panel.values() for gene in genes])]

        # Resetting the index to retain the original index values
        filtered_df.reset_index(drop=True, inplace=True)

        return filtered_df
    except Exception as e:
        # Print an error message if reading the file fails
        print(f"Error reading the file: {e}")
        return None