manipulate text using shell script?

Question

How can i manipulate the text file using shell script?

input

chr2:98602862-98725768
chr11:3100287-3228869
chr10:3588083-3693494
chr2:44976980-45108665

expected output

2 98602862 98725768
11 3100287 3228869
10 3588083 3693494
2 44976980 45108665

what is the logic here? try to describe it in a way that makes sense and also provide your attempts, since this seems quite basic. — fedorqui
– fedorqui, Commented Jun 25, 2015 at 14:57

nu11p01n73R · Accepted Answer · 2015-06-25 15:20:33Z

1

Using sed you can write

$ sed 's/chr//; s/[:-]/ /g' file
2 98602862 98725768
11 3100287 3228869
10 3588083 3693494
2 44976980 45108665

Or maybe you could use awk

awk -F "chr|[-:]" '{print $2,$3, $4}' file
2 98602862 98725768
11 3100287 3228869
10 3588083 3693494
2 44976980 45108665

What it does

-F "chr|[-:]" sets the field separators to chr or : or -. Now you could print the different fields or columns.
You can also use another field separator as -F [^0-9]+ which will makes anything other than digits as separators.

answered Jun 25, 2015 at 15:01

nu11p01n73R

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2 Comments

Alternatively using awk, the field separator could be [^0-9]+ (i.e. one or more non-digits).

@TomFenech Good point.Added to a answer. Thanks for the tip :)

Ed Morton · Accepted Answer · 2015-06-25 16:19:07Z

1

If you don't care about a leading blank char:

$ tr -s -c '[0-9\n]' ' ' < file
 2 98602862 98725768
 11 3100287 3228869
 10 3588083 3693494
 2 44976980 45108665

answered Jun 25, 2015 at 16:05

Ed Morton

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