Question

I have to do a simple task, but I don’t know how to do it and I’m staked. I need to intersperse the lines of two different files each 4 lines:

File 1:

1
2
3
4
5
6
7
8
9
10
11
12

FILE 2:

A
B
C
D
E
F
G
H
I
J
K
L

Desired result:

1
2
3
4
A
B
C
D
5
6
7
8
E
F
G
H
9
10
11
12
I
J
K
L

I’m looking for a sed, awk or python script, or any other bash command.

Thanks for your time!!

I tried to do it using specific python libraries that recognize the 4 lines modules of each files. But It doesn’t work and now I trying to do it without this libraries, but don’t know how.

import sys
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord


def main(forward,reverse):

    for F, R in zip ( SeqIO.parse(forward, "fastq"), SeqIO.parse(reverse, "fastq") ):

        fastq_out_F = SeqRecord( F.seq, id = F.id, description = "" )
        fastq_out_F.letter_annotations["phred_quality"] = F.letter_annotations["phred_quality"]

        fastq_out_R = SeqRecord( R.seq, id = R.id, description = "" )
        fastq_out_R.letter_annotations["phred_quality"] = R.letter_annotations["phred_quality"]

        print fastq_out_F.format("fastq"),
        print fastq_out_R.format("fastq"),


if __name__ == '__main__':
    main(sys.argv[1], sys.argv[2])  

Answer 1

This might work for you:(using GNU sed)

sed -e 'n;n;n;R file2' -e 'R file2' -e 'R file2' -e 'R file2' file1

or using paste/bash:

paste -d' ' <(paste -sd'   \n' file1) <(paste -sd'   \n' file2) | tr ' ' '\n'

or:

parallel -N4 --xapply 'printf "%s\n%s\n" {1} {2}'  :::: file1 :::: file2