merge_bcs_reads.py

#!/usr/bin/python3
"""
Description: Will write the barcodes at the beginning of the output file.

Usage:
python merge_bcs_reads.py X Y Z
X: barcodes fastq file
Y: reads fastq file
Z: merged output file
"""
from sys import argv
from cogent.parse.fastq import MinimalFastqParser


bcs = open(argv[1], "U")
reads = open(argv[2], "U")
combined_out = open(argv[3], "w")

header_index = 0
sequence_index = 1
quality_index = 2
for bc_data, read_data in zip(MinimalFastqParser(bcs, strict=False),
                              MinimalFastqParser(reads, strict=False)):
    curr_label = bc_data[header_index].strip()
    bc_read = bc_data[sequence_index]
    bc_qual = bc_data[quality_index]
    seq_read = read_data[sequence_index]
    seq_qual = read_data[quality_index]
    combined_out.write("@%s\n" % curr_label)
    combined_out.write("%s\n" % (bc_read + seq_read))
    combined_out.write("+\n")
    combined_out.write("%s\n" % (bc_qual + seq_qual))