convert_to_presence_absence.py

from pathlib import Path
import PySimpleGUI as sg
import pandas as pd
from taxontabletools.taxontable_manipulation import strip_metadata
from taxontabletools.taxontable_manipulation import collect_metadata
from taxontabletools.taxontable_manipulation import add_metadata

def convert_to_presence_absence(TaXon_table_xlsx, path_to_outdirs):

    ## load TaxonTable
    TaXon_table_xlsx = Path(TaXon_table_xlsx)
    TaXon_table_df = pd.read_excel(TaXon_table_xlsx).fillna('')
    TaXon_table_df_metadata = collect_metadata(TaXon_table_df)
    TaXon_table_df = strip_metadata(TaXon_table_df)

    # create presence/absence table
    presence_absence_list = []
    for col in TaXon_table_df.values.tolist():
        presence_absence_list.append(col[0:10] + [int(1) if reads != 0 else int(0) for reads in col[10:]])

    ## create a new dataframe
    df_pa = pd.DataFrame(presence_absence_list)
    df_pa.columns = TaXon_table_df.columns.tolist()

    # add metadata columns
    df_pa = add_metadata(df_pa, TaXon_table_df_metadata)

    ## write table
    output_file = Path(str(path_to_outdirs) + "/" + "TaXon_tables" + "/" + TaXon_table_xlsx.stem + "_pa.xlsx")
    df_pa.to_excel(output_file, index=False, sheet_name = 'TaXon table')

    closing_text = "Presence absence tables is found in: " + str(path_to_outdirs) + "/TaXon_tables/"
    sg.Popup(closing_text, title="Finished", keep_on_top=True)
    from taxontabletools.create_log import ttt_log
    ttt_log("presence absence conversion", "processing", TaXon_table_xlsx.name, output_file.name, "nan", path_to_outdirs)