Manipulate Csv File Using Bash Script or Python, Converting Certain Columns into Rows

Here's an awk approach:

$ awk 'NR>1{for(i=1;i<=NF;i++){ if((i%4)==0) printf "\n"; printf "%s%s",$i,FS;}printf "\n"} END{printf "\n"}' input.csv
chr16 2697996 2697997 
chr16 2086192 2086193 
chr5 112801382 112801383 
chr5 138445682 138445683 
chr15 26869333 26869334 
chr8 119416385 119416386

Assuming the "Columns" is present in the file, it'd be easier to process the file without them, hence NR>1 part. After that is a simple for-loop, which inserts a newline whenever there's no remainder in integer division by 4 in the column number ( the (i%4) == 0 part ). This is a very common trick to deal with short counters or data that needs to occur at specific intervals. Newline is necessary because we're printing data via printf directly as plain string, not a full line.

Since you've requested python, here's a python script as well:

#!/usr/bin/env python3
import sys

with open(sys.argv[1]) as fd:
    for index,line in enumerate(fd):

        items=line.strip().split()
        if index == 0:
            print(" ".join(items[:len(items)//2]))
            continue

        left = items[:len(items)//2]
        right = items[len(items)//2:]
        print( " ".join(left) )
        print( " ".join(right) )

Works as follows:

$ ./break_columns.py ./input.csv 
Column1 Column2 Column3
chr16 2697996 2697997
chr16 2086192 2086193
chr5 112801382 112801383
chr5 138445682 138445683
chr15 26869333 26869334
chr8 119416385 119416386

You can use Miller () and a bash script. Starting from input

Column1   Column2    Column3     Column4    Column5      Column6
chr16    2697996    2697997     chr16      2086192      2086193
chr5    112801382   112801383   chr5       138445682    138445683
chr15   26869333    26869334    chr8       119416385    119416386

and running

<input tail -n +2 | mlr --nidx --ifs ' ' --repifs cut -f 1,2,3 >out_01
<input tail -n +2 | mlr --nidx --ifs ' ' --repifs cut -f 4,5,6 >out_02

mlr --nidx --ifs ' ' --repifs cat out_01 out_02 >out

mlr -I --n2c --fs ' ' cat then label Column1,Column2,Column3 out

you will have

Column1 Column2 Column3
chr16 2697996 2697997
chr5 112801382 112801383
chr15 26869333 26869334
chr16 2086192 2086193
chr5 138445682 138445683
chr8 119416385 119416386

If you want a pretty printed output, change the final command in mlr -I --n2p --fs ' ' cat then label Column1,Column2,Column3 out

Column1 Column2   Column3
chr16   2697996   2697997
chr5    112801382 112801383
chr15   26869333  26869334
chr16   2086192   2086193
chr5    138445682 138445683
chr8    119416385 119416386