Samplesheet_converter_v1.1.py

# These scripts are for the purpose of converting Illumina samplesheet that contains Chromium 10X indexes for demultiplexing.
# Headers and lines with ordinary indexes will be passed without any change. Lines with Chromium 10X indexes will be expanded into 4 lines, with 1 index in each line, and suffix 'Sx' will be added at the end of sample names.
# Example:
# ------------------------------------------------------------------------------------------------------
# Script: python main.py -i <inputfile> -o <outputfile> -x <indexlibrary>
# ------------------------------------------------------------------------------------------------------
# Original samplesheet:
# [Header]
# Date,None
# Investigator Name,Chuan Wang
# Experiment Name,Project_001
# [Reads]
# 151
# 151
# [Data]
# Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description
# 1,Sample_101,101,HGWT5ALXX,1:1,SI-GA-A1,,Project_001,
# ------------------------------------------------------------------------------------------------------
# Modified samplesheet:
# [Header]
# Date,None
# Investigator Name,Chuan Wang
# Experiment Name,Project_001
# [Reads]
# 151
# 151
# [Data]
# Lane,SampleID,SampleName,SamplePlate,SampleWell,index,index2,Project,Description
# 1,Sample_101_S1,101_S1,HGWT5ALXX,1:1,GGTTTACT,,Project_001,
# 1,Sample_101_S2,101_S2,HGWT5ALXX,1:1,CTAAACGG,,Project_001,
# 1,Sample_101_S3,101_S3,HGWT5ALXX,1:1,TCGGCGTC,,Project_001,
# 1,Sample_101_S4,101_S4,HGWT5ALXX,1:1,AACCGTAA,,Project_001,
# ------------------------------------------------------------------------------------------------------

# Samplesheet_convert_v1.1
# Written by Chuan Wang (chuan-wang@github), 2017-03-08

#!/usr/bin/python

import sys
import csv
import argparse

# Read index library
def read_index_library(indexlibrary):
    with open(indexlibrary,mode='r') as input_file:
        indexes = csv.reader(input_file)
        index_library = {rows[0]:[rows[1],rows[2],rows[3],rows[4]] for rows in indexes}
    return index_library

# Modify samplesheet
def modify_samplesheet(inputfile,indexlibrary):
    index_library=read_index_library(indexlibrary)
    modified_samplesheet=[]
    with open(inputfile,mode='r') as org:
        samplesheet = csv.reader(org)
        header_flag = True
        for row in samplesheet:
            # Looking for the header '[Data]'
            if header_flag:
                if '[Data]' not in row:
                    modified_samplesheet.append(row)
                else:
                    # Jump to the row with column names, specify the variable index of 'index'
                    row = next(samplesheet)
                    index1 = row.index("index")
                    modified_samplesheet.append(row)
                    header_flag = False
            # Working with the body part of samplesheet
            else:
                if row[index1] not in index_library:
                    modified_samplesheet.append(row)
                else:
                    index_count = 1
                    org_row = row[:]
                    for index in index_library[row[index1]]:
                        row[1] += '_S'
                        row[1] += str(index_count)
                        row[2] += '_S'
                        row[2] += str(index_count)
                        row[index1] = index
                        modified_samplesheet.append(row)
                        index_count += 1
                        row = org_row[:]
    return modified_samplesheet

# Write new samplesheet
def write_new_samplesheet(modified_samplesheet,outputfile):
    with open(outputfile,mode='w') as new_samplesheet:
        writer=csv.writer(new_samplesheet)
        for row in modified_samplesheet:
            writer.writerow(row)

# Main
def main(argv):
    inputfile = args.inputfile
    outputfile  = args.outputfile
    indexlibrary = args.indexlibrary

    modified_samplesheet = modify_samplesheet(inputfile,indexlibrary)
    write_new_samplesheet(modified_samplesheet,outputfile)

if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('-i', dest="inputfile", help="Original samplesheet", type=str, required=True, default=False)
    parser.add_argument('-o', dest="outputfile", help="Output modified samplesheet", type=str, required=True, default=False)
    parser.add_argument('-x', dest="indexlibrary", help="Index library", type=str, required=True, default='Chromium_10X_indexes')
    args = parser.parse_args()

    main(args)