Question

Fq file to table

0

Entering edit mode

3.9 years ago

poltora4enko ▴ 10

Hello all!

I am looking for different ways to convert fq file to tabular format. I mean from this:

@name
AGTC
some_text
HHJH

to this:

@some_name   AGTC   +   HHHH

every four strings in one row

How can I do it with Python/R and in bash/awk?

fastq • 1.6k views

ADD COMMENT • link updated 2.3 years ago by Ram 45k • written 3.9 years ago by poltora4enko ▴ 10

GenoMax · Accepted Answer · 2021-12-02

4

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3.9 years ago

Pierre Lindenbaum 166k

man paste

cat fastq | paste  - - - -

ADD COMMENT • link updated 3.9 years ago by GenoMax 154k • written 3.9 years ago by Pierre Lindenbaum 166k

score 2 · Accepted Answer · 2021-12-02

2

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3.9 years ago

Alex Reynolds 36k

In Python:

#!/usr/bin/env python

import sys

record = []
for line in sys.stdin:
    record.append(line.rstrip())
    if len(record) == 4:
        sys.stdout.write('{}\n'.format('\t'.join(record)))
        record.clear()

Then: python ./linearize_fastq.py < in.fastq > out.txt

ADD COMMENT • link 3.9 years ago by Alex Reynolds 36k

score 2 · Accepted Answer · 2021-12-03

2

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3.9 years ago

cpad0112 21k

$ awk -v OFS="\t" -v RS="@" 'NR > 1 {print "@"$1,$2,$3,$4}' test.fq
$ awk -v OFS="\t" -v RS="@" 'NR > 1 {gsub("\n","\t"); print "@"$0}' test.fq
$ bioawk -c fastx '{print $seq, $name, $qual}' test.fq
$ seqkit fx2tab test.fq
$ tr -s "\n" "\t" < test.fq | sed -r 's/\t@/\n@/g'

ADD COMMENT • link 3.9 years ago by cpad0112 21k