[Python] reads from fastq file

Question

[thebioinfo]

I am looking for the fastest python code to extract only reads from fastq file and store it in new file.

[WouterDeCoster]

to extract only reads from fastq file and store it in new file

What do you want to do?

[thebioinfo]

as a beginner of python, i just need to learn how to do it.

[WouterDeCoster]

You just want to copy all reads to a new file?

[thebioinfo]

yes i want to copy all reads to a new file

[Buffo]

Do you mean fastq to fasta?

[thebioinfo]

yes fastq to fasta.....

[WouterDeCoster]

Well, you better be a more precise next time when asking questions.

Answer 1

[said3427]

from Bio import SeqIO

SeqIO.convert('myfile.fastq','fastq','myoutput.fasta','fasta')

Answer 2

[Alex Reynolds]

$ python -c "import subprocess; subprocess.check_call(\"awk '{ if (NR%4==1) { print \\\">\\\"\$0; } else if (NR%4==2) { print \$0; } }' source.fq > destination.fa\", shell=True)"

Or:

#!/usr/bin/env python
import subprocess
subprocess.check_call("awk '{ if (NR%4==1) { print \">\"$0; } else if (NR%4==2) { print $0; } }' source.fq > destination.fa", shell=True)

[WouterDeCoster]

While technically correct and probably the most efficient, it doesn't really teach OP something about Python :-p

[Alex Reynolds]

Doing things on the command line is going to be the fastest route, so the subprocess library is useful to know, if the asker is forced to use Python.

Answer 3

[WouterDeCoster]

this is a general code snippet to copy files, what you are asking for... but quite useless in my opinion.

with open("myfile.fastq") as infile, open("myoutput.fastq", 'w') as output:
    for line in infile:
        output.write(line)

[grant.hovhannisyan]

I guess @thebioinfo wants only reads, so each 4the line.

Answer 4

[Buffo]

As you are looking for fastq to fasta, I think t is a duplicated question here

If you want to learn some python you may try:

import sys
filename = sys.argv[1]

with open(filename, "r") as infile:
    line_ct = 0
    for line in infile:
        if (line_ct % 4 == 0):
            print(">" + line[1:], end="")
            line_ct = 0
        if (line_ct  == 1):
            print(line, end = "")
        line_ct += 1