Format samplesheet to use in bcl2fastq

reverse-sample-sheet.py

from Bio.Seq import Seq
import pandas as pd
import csv
import sys
import os

def reverse_complement(sequence):
    """
    Give me the sequence and I give you the reverse-complement of it
    """
    seq = Seq(str(sequence))
    reverse = str(seq.reverse_complement())
    return reverse

def main():
    path, arq = os.path.split(os.path.abspath(sys.argv[1]))
    sample_sheet = path+"/"+arq
    new_arq = path+"/"+arq.split(".")[0]+"-new.csv"

    # Organize the DataFrame with the reverse complement
    sample_df = pd.read_csv(sample_sheet, skiprows=20)
    sample_df["index2"] = sample_df["index2"].apply(reverse_complement)

    with open(sample_sheet) as master, open(new_arq, "w") as matched:
        cr = csv.reader(master)
        cw = csv.writer(matched)
        for i in range(20):
            cw.writerow(next(cr))
        sample_df.set_index("Sample_ID").to_csv(matched)

if __name__ == "__main__":
    main()