Shell – Splitting a sequence into fixed width

awkshell-scripttext processing

I have a file like this which is a two-column tab-separated file.

CTGCAGTTTCCCCAAATGTGGGAAACTTGACTGTATAATTTGTGGCAGTGGTA   a1
GATTTCCCCAAATGTGGGAAACTCACTCGGCAGGCGTTGATA  a2

I want to get an output like this:

>a1
CTGCAGTTTCCCCAAATGTG
GGAAACTTGACTGTATAATT
TGTGGCAGTGGTA
>a2
GATTTCCCCAAATGTGGGAA
ACTCACTCGGCAGGCGTTGA
TA

I was trying to use the fold command inside awk. Is it possible to use another command within awk?

Also, the width of each line I want is 15, so I tried something like this, but it didn't work:

awk -F "\t" '{a=$(fold -w 50 $1);print a,$2}' file.txt

How can I do this?

Best Answer

With python test.py < input and test.py:

import sys
for i in sys.stdin:
     s, ident = i.rstrip().split()
     print '>{0}'.format(ident)
     while s:
          print s[:15]
          s = s[15:]

Related Solutions

Splitting a file with lines separated by tabs into two files

A solution could be:

awk '{ print $1 > "file1"; print $2 > "file2"}' file

Splitting a single file into multiple files based on matching strings in Linux

I am sure there is an awk command that can do this, I am not skilled enough in awk to come up with a solution. In the meantime, you could use something like this:

#!/bin/bash

csplit -z tosplit /661/ {*}

for file in xx*; do
    newName=$(egrep -o '2[0-9]{7}' $file)
    mv $file $newName.txt
done
rm -rf xx*

Where tosplit is this file (your example file):

661###############20160315###
###########################
###########################
661###############20160316###
###########################
661###############20160317###
###########################

After running this script (in the same directory as the tosplit file) I get three files:

ls 2016031*
20160315.txt  20160316.txt  20160317.txt

...looking like this:

cat 20160315.txt 
661###############20160315###
###########################
###########################

cat 20160316.txt 
661###############20160316###
###########################

cat 20160317.txt 
661###############20160317###
###########################

You can possibly(?) use csplit to name the files as well, but that too is above my paygrade!

Best Answer

Related Solutions

Splitting a file with lines separated by tabs into two files

Splitting a single file into multiple files based on matching strings in Linux

Related Question