Question

FASTQ to FASTA converter: Implement a FASTQ to FASTA file format converter in python (the input is a FASTQ file and the output is a FASTA file)

Answer 1

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FASTQ to FASTA converter: Implement a FASTQ to FASTA file format converter in python (the input is a FASTQ file and the output is a FASTA file)

SOL::-

''' This is how you have to run the code on cmd

create one fastqToFasta.py with this code

then the fastq file with gz extension

and give the name of fasta file in the command '''

#python fastqToFasta.py fastq.gz fasta gz

import sys, subprocess, gzip
from subprocess import PIPE

infile = sys.argv[1]
fasta = sys.argv[2]
gz = sys.argv[3]

## if gz is present open it with the gzip library else normal
if '.gz' in infile:
   print("detected a .gz file")
   fastq = gzip.open(infile, 'rb')
else:
   fastq = open(infile, 'r')

## main function

def main(fastq, fasta, gz):
   line_n =0
   line_buffer = 0
   line_id = 1
   if gz: ### if gz argument is provided it will write out a gz file else normal
       outfile = gzip.open(fasta+'.gz', 'w')
   else:
       outfile = open(fasta, 'w')
   fastas = 1
   fasta_length =0
   for line in fastq:
       line_n += 1
           #line_id += 1
       if line_n == 10000:
           line_buffer += 10000
           line_n =0
           print ('processed lines ', line_buffer)
       if line_id == 4:
           line_id = 1
       elif line_id == 3:
           line_id += 1
       elif line_id == 2:
           line_id += 1
           fasta_line = line
           fasta_length += len(fasta_line.strip())
           outfile.write(fasta_line)
           fastas += 1
       else:
           if '@' not in line:
               print ('are you sure this is a fastq ??')
           else:
               fasta_header = line.replace('@', '>')
               line_id += 1
               outfile.write(fasta_header)
   outfile.close()
   print ('FASTA records written', fastas, 'average length of fasta sequences ', float(fasta_length//fastas))

if __name__ == '__main__':
   main(fastq, fasta, gz)

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THANK YOU...!!