convertHeaders.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import argparse
import gzip

# Rewrite as illumina header
def convertIllumina(elements_dict):
    template_str = "@{instrument}:{run_number}:{flowcell_id}:{lane}:{tile}:{x_pos}:{y_pos} {read}:N:0:{sample_barcode}\n"
    formatted_string = template_str.format(instrument = elements_dict["instrument"],
                                           run_number = elements_dict["run_number"],
                                           flowcell_id = elements_dict["flowcell-id"],
                                           lane = elements_dict["lane"],
                                           tile = elements_dict["tile"],
                                           x_pos = elements_dict["x-pos"],
                                           y_pos = elements_dict["y-pos"],
                                           read = elements_dict["read_no"],
                                           sample_barcode = elements_dict["sample_barcode"])
    return(formatted_string)


# Collect elements from BGI format
# Please note that you will need to attach the sample barcode sequence 
# to the headers of the input FASTQ file
# eg. 
def parseBGI(header):
    # Extract sample barcode sequence
    if header[-10] == "_":
        # Get sample barcode
        header_split1 = header.split("_")
        sample_barcode = header_split1[-1]
        header = header.replace("_" + sample_barcode, "")

        # Get basic information from split
        # Takes into account presence of sample name
        # Even if the sample name has underscores, it will take the
        # last set of values which will be the header information
        if "_" in header:
            header = header.split("_")
            header_split1 = header[-1]
        else:
            header_split1 = header
        
        header_split2 = header_split1.split("/")
        paired_read_direction = int(header_split2[1])

        # Get rest of the information from the header
        seq_header = header_split2[0]
        seq_header = seq_header.replace("@", "")

        # First 10 charcters of sequence header, after sample number
        # are the flowcell number
        flowcell_id = seq_header[:10]
        
        # Followed by flowcell 
        lane_id = seq_header[10:12]
        lane_id = int(lane_id.replace("L", ""))
        
        # Get location of C (x location)
        x_id = seq_header[12:16]
        x_id = int(x_id.replace("C", ""))

        # Get location of R (y location)
        y_id = seq_header[16:20]
        y_id = int(y_id.replace("R", ""))

        # Get run number (last part of the string)
        tile_number = int(seq_header[20:])

        # Pack into dictionary
        elements_dict = {"instrument": "MGISEQ-2000", "run_number": 1, "sample_barcode": sample_barcode, "lane": lane_id, "x-pos": x_id, "y-pos": y_id, "tile": tile_number, "flowcell-id": flowcell_id, "read_no": paired_read_direction}
        return elements_dict

    else:
        print("Sample index barcode not detected. Please check you have attached the barcode with attachBarcodes.sh.")
        sys.exit()

# Parses the entry
def parseLine(x):
    if x.startswith("@"):
        elements_dict = parseBGI(x)
        converted_header = convertIllumina(elements_dict)
        return(converted_header)
    else:
        return(x)

def open_file(input_file, mode = "rb"):
    if ".gz" in input_file:
        input_fastq = gzip.open(input_file, mode)
    else:
        input_fastq = open(input_file, mode)
    return(input_fastq)

# Retrieves arguments inputted by user
def parseArguments(args):
    # Retrieve from parser
    input_file = args.input
    output_file = args.output
  
    # Extract barcode from filename
    return input_file, output_file

# Sets up arguments for user input
def setupParser():
    # Set up argument parser
    parser = argparse.ArgumentParser()
    parser.add_argument("-i", "--input", action = "store", help = "fastq.gz file generated by BGI platform.", type = str, required = True)
    parser.add_argument("-o", "--output", action = "store", help = "Name of output converted file.", type = str, required = True)
    args = parser.parse_args()

    return(args)

# Code starts here
if __name__ == "__main__":
    args = setupParser()
    input_file, output_file = parseArguments(args)
    input_fastq = open_file(input_file, "rt")
    output_fastq = open_file(output_file, "wt")

    for line in input_fastq:
        parsed_line = parseLine(line)
        output_fastq.write(parsed_line)
    
    input_fastq.close()
    output_fastq.close()
    print("Conversion of %s complete!" % input_file)