Cut the spaces and hyphen from a text file

Question

The text file I have now looks like this,

VOG0005              -          k141_44786_1         -            4.9e-11   41.0   0.0     2e-08   32.4   0.0   2.0   2   0   0   2   2   2   2 -   
VOG0005              -          k141_46357_20        -            9.2e-44  148.8   1.7   2.4e-32  111.2   0.2   3.0   2   1   1   3   3   3   3 -   
VOG0010              -          k141_1081_2          -            1.2e-06   27.4   0.5   0.00011   21.0   0.0   2.3   2   0   0   2   2   2   2 -
VOG0010              -          k141_17432_67        -            1.2e-07   30.7   0.0   1.7e-07   30.2   0.0   1.3   1   1   0   1   1   1   1 -
VOG0010              -          k141_2610_7          -            2.1e-06   26.6   0.0   2.9e-06   26.2   0.0   1.1   1   0   0   1   1   1   1 

Does the sort command count the hyphen and the spaces in between as separate columns? If yes, then how can I use the cut command to remove the hyphen in between?

VOG0005 - k141_44786_1 - 4.9e-11

to get something like this

VOG0005 k141_44786_1 4.9e-11

i.e., with a single space would work for me. I have tried one command: cut -f2 File.txt, but it doesn't seem to work in my case.

Can anyone help please?

Answer 1

You can use sed command to remove the hyphen with spac.

sed 's/- //g'

Please refer the below example

# cat example.txt
VOG0005 - k141_44786_1 - 4.9e-11 41.0 0.0 2e-08 32.4 0.0 2.0 2 0 0 2 2 2 2 -
VOG0005 - k141_46357_20 - 9.2e-44 148.8 1.7 2.4e-32 111.2 0.2 3.0 2 1 1 3 3 3 3 -
VOG0010 - k141_1081_2 - 1.2e-06 27.4 0.5 0.00011 21.0 0.0 2.3 2 0 0 2 2 2 2 -
VOG0010 - k141_17432_67 - 1.2e-07 30.7 0.0 1.7e-07 30.2 0.0 1.3 1 1 0 1 1 1 1 -
VOG0010 - k141_2610_7 - 2.1e-06 26.6 0.0 2.9e-06 26.2 0.0 1.1 1 0 0 1 1 1 1 -

# sed 's/- //g' example.txt
VOG0005 k141_44786_1 4.9e-11 41.0 0.0 2e-08 32.4 0.0 2.0 2 0 0 2 2 2 2 -
VOG0005 k141_46357_20 9.2e-44 148.8 1.7 2.4e-32 111.2 0.2 3.0 2 1 1 3 3 3 3 -
VOG0010 k141_1081_2 1.2e-06 27.4 0.5 0.00011 21.0 0.0 2.3 2 0 0 2 2 2 2 -
VOG0010 k141_17432_67 1.2e-07 30.7 0.0 1.7e-07 30.2 0.0 1.3 1 1 0 1 1 1 1 -
VOG0010 k141_2610_7 2.1e-06 26.6 0.0 2.9e-06 26.2 0.0 1.1 1 0 0 1 1 1 1 -

Answer 2

Similar to sed, you can also do it using perl:

$ cat File.txt | tr -s " " | perl -pe 's/[[:space:]]-//g' | sponge File.txt
VOG0005 k141_44786_1 4.9e-11 41.0 0.0 2e-08 32.4 0.0 2.0 2 0 0 2 2 2 2
VOG0005 k141_46357_20 9.2e-44 148.8 1.7 2.4e-32 111.2 0.2 3.0 2 1 1 3 3 3 3
VOG0010 k141_1081_2 1.2e-06 27.4 0.5 0.00011 21.0 0.0 2.3 2 0 0 2 2 2 2
VOG0010 k141_17432_67 1.2e-07 30.7 0.0 1.7e-07 30.2 0.0 1.3 1 1 0 1 1 1 1
VOG0010 k141_2610_7 2.1e-06 26.6 0.0 2.9e-06 26.2 0.0 1.1 1 0 0 1 1 1 1

or

<File.txt tr -s " " | perl -pe 's/[[:space:]]-//g' | sponge File.txt

# on fish shell
tr -s " " <File.txt | perl -pe 's/[[:space:]]-//g' | sponge File.txt

Explanation

tr -s " "                    
# Removes extra spaces
perl -pe 's/[[:space:]]-//g' 
# Replaces any ' -' with nothing
sponge File.txt              
# Reads standard input and writes it out to the specified file.

---

Apparently you can achieve the same result using only perl (thanks @Stéphane Chazelas) :

perl -pi -e 's/ +/ /g; s/[[:space:]]-//g' File.txt

similarly sed:

sed -i -E 's/ +/ /g; s/[[:space:]]-//g' File.txt

see @Stéphane Chazelas comment for explanation

Answer 3

First of all, yes, sort will regard the first - as being column 2, the k141_xxxx as column 3, the second - as column 4, etc.  But that’s an incomplete oversimplification; the truth is subtle and complex.

Your question is not entirely clear.  To clobber the second and fourth columns, whatever they are, do

awk '{ $2=""; $4=""; print }' example.txt

To clobber any fields that are a hyphen, do

awk '{for (i=1; i<=NF; i++) if ($i == "-") $i = ""; print}' example.txt

awk is overkill (but then, so is perl).