fastq2json.py

import sys
import json
import os
import re
from os.path import join
import argparse
from collections import defaultdict

def fastq_json(fastq_dir):
    args=fastq_dir
    FILES = defaultdict(lambda: defaultdict(list))
## build the dictionary with full path for each fastq.gz file
    for root, dirs, files in os.walk(args):
        for file in files:
            if file.endswith("fq.gz"):
                full_path = join(root, file)
                #R1 will be forward reads, R2 will be reverse reads
                m = re.search(r"(.+).(R[12]).fq.gz", file)
                if m:
                    sample = m.group(1)
                    reads = m.group(2)  
                    FILES[sample][reads].append(full_path)
                    
    print()
    print ("total {} unique samples will be processed".format(len(FILES.keys())))
    print ("------------------------------------------")
    for sample in FILES.keys():
        for read in FILES[sample]:
            print ("{sample} {read} has {n} fastq".format(sample = sample, read = read, n = len(FILES[sample][read])))
    print ("------------------------------------------")
    print("check the samples.json file for fastqs belong to each sample")
    print()
    
    js = json.dumps(FILES, indent = 4, sort_keys=True)
    open('samples.json', 'w').writelines(js)
       
if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("--fastq_dir", help="Required. the FULL path to the fastq folder")
    args = parser.parse_args()
    fastq_json(args.fastq_dir)
    assert args.fastq_dir is not None, "please provide the path to the fastq folder"