Takes a demultiplexed fastq file as input and returns sorted list of barcodes found in ascending order of frequency.

count-barcode-freq.py

## Usage: python3 count-barcode-freq.py <fastq_file.gz>
## Example: python3 count-barcode-freq.py sample.fastq.gz
from operator import itemgetter
import sys, gzip

barcodes = {}
with gzip.open(sys.argv[1]) as fastq:
        for line in fastq:
                if not line.startswith(b'@'): continue
                bc = line.decode("utf-8").split(':')[-1].strip()
                if bc not in barcodes:
                        barcodes[bc] = 1
                else:
                        barcodes[bc]+=1

total = sum(barcodes.values())
for k, v in sorted(barcodes.items(), key=itemgetter(1)):
        print(k, v, round(v/total*100, 2))

How do I import a Fastq file for this script?

How do I import a Fastq file for this script?

Simply pass the fastq file as an argument:
python3 count-barcode-freq.py sample.fastq.gz

I've updated the script to include a usage example.

Hello Dr. Khalfan,
Thank you for making your code public on GitHub. I have run this python script on one of my files and am getting the output:
15 849464 100.0

The first four lines of my fastq.gz file is:

@FS10000408:4:BNT40310-1714:1:1101:1050:1000 1:N:0:15
GGTTTGCTCTGGTTATTGAAACTTCTTGACTGTGTTCTCTTGATTTTCCCCGGTTTGATAGTTTAGCCGGCTTTGCTTCATTCTTCAGCGAAGTGGCAAATCTAGCCAATAACAAAAAAGTCAAGGAGGTGGTTTTCTACTGGAAGTAC
+
,,FFF,FFFFFFFFFFF,FFFFF:FFF,F:F:F,FFFFFFF,F:FFFF,F,,:FF,:,FF,F:,F:FFF::FFFF:F,:FFFFF,F,,::FF:FF,FF:,FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF

I was expecting an oligonucleotide not a numeral as the barcode... could you give me some guidance? These reads were made on an Illumina iSeq machine using Nextera adapters.

Thank you for your time!
Best Regards,
René