vendredi 26 août 2016

BASH - Summarising information from several fields in unique field using Loop and If statements

I have the following tab-separated file:

A1      A1      0       0       2       1       1 1     1 1     1 1     2 1     1 1
A2      A2      0       0       2       1       1 1     1 1     1 1     1 1     1 1
A3      A3      0       0       2       2       1 1     2 2     1 1     1 1     1 1
A5      A5      0       0       2       2       1 1     1 1     1 1     1 2     1 1

The idea is to summarise the information between column 7 (included) and the end in a new column that is added at the end of the file.

To do so, these are the rules:

  • If the total number of “2”s in the row (between column 7 and the end) is 0: add “1 1” to the new last column

  • If the total number of “2”s in the row (between column 7 and the end) is 1: add “1 2” to the new last column

  • If the total number of “2”s in the row (between column 7 and the end) is 2 or more: add “2 2” to the new last column

I started to extract the columns I want to work on using the command:

awk '{for (i = 7; i <= NF; i++) printf $i " "; print ""}' myfile.ped > tmp_myfile.txt

Then I count the number of occurrence in each row using:

sed 's/[^2]//g' tmp_myfile.txtt | awk '{print NR, length }' > tmp_occurences.txt

Which outputs:

1 1
2 0
3 2
4 1

Then my idea was to write a for loop that loops through the lines to add the new summary column. I was thinking in this kind of structure, based on what I found here: http://ift.tt/2c16YTR:

while read line ;
do
    set $line

    If ["$2"==0]
    then
        $3=="1 1"

    elif ["$2"==1 ]
    then
        $3=="1 2”

    elif ["$2">=2 ]
    then 
        $3==“2 2”

    else
        print ["error"]

    fi
done < tmp_occurences.txt

But I am stuck here. Do I have to create the new column before starting the loop? Am I going in the right direction?

Ideally, the final output (after merging the first 6 columns from the initial file and the summary column) would be:

A1      A1      0       0       2       1       1 2
A2      A2      0       0       2       1       1 1
A3      A3      0       0       2       2       2 2
A5      A5      0       0       2       2       1 2 

Thank you for your help!

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