Fq file to table
3
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
• 1.1k views
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
$ 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'
Login before adding your answer.
Traffic: 949 users visited in the last hour