show_missing_rows_between_2_tables.py

"""
Output rows from table1 that are missing from table2 i.e. table1 - table2, use
given columns to determine 'missing'
"""
import argparse
import pandas as pd
import sys


def output_missing_rows(t1, t2, join_columns, delimiter, output_only_columns):
    df1 = pd.read_csv(t1, sep=delimiter)
    df2 = pd.read_csv(t2, sep=delimiter)
    df1i = df1.set_index(join_columns)
    df2i = df2.set_index(join_columns)
    if output_only_columns is None:
        df1i.ix[pd.Index(set(df1i.index) - set(df2i.index)),
                :].to_csv(sys.stdout, sep=delimiter)
    else:
        df1i.ix[pd.Index(set(df1i.index) - set(df2i.index)),
                output_only_columns].to_csv(sys.stdout, sep=delimiter)

def main():
    parser = argparse.ArgumentParser(description=__doc__,
                                        formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument("table1", type=str, help="TSV")
    parser.add_argument("table2", type=str, help="Excel output")
    parser.add_argument("column_names", type=str, nargs='+', help="Which columns to join on")
    parser.add_argument("-c", "--output_only_columns", type=str, default=None, nargs='+', help="Which columns to output")
    parser.add_argument("-d", "--delimiter", type=str, default="\t", help="Set delimiter")
    args = parser.parse_args()
    output_missing_rows(args.table1, args.table2, args.column_names, args.delimiter, args.output_only_columns)

if __name__ == "__main__":
    main()