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Full Discussion: Reading from file bash command
Top Forums Shell Programming and Scripting Reading from file bash command Post 303003163 by jim mcnamara on Friday 8th of September 2017 08:29:04 AM
Old 09-08-2017
This statement means that if there is no gene2 then there cannot be a gene3 read:
Code:
 [ -z "$gene2" ] && continue

When you use the read statement you have to have all fields there in order to get gene3.

Otherwise gene3 is an "empty" variable. Or the same can happen for gene2.

You can create dummy values for those variables if they are empty, but since you have a separate script processing things that could affect the output of that script.

Try creating an intermediate file with dummy variables, let's use the word 'dummy' for the values of empties. This is awk, the output file will be called tmp.tmp which is what your script will have to use for input.

This could also be set up writing to a pipe which your existing script reads.
Code:
awk '{
        # check to see what type of line we have, 
        # if  col 1 is a number then we have to play the dummy game
        if( int($1) !=0)
        {
            if(NF==6) { $7="dummy"; $8="dummy" }
            if(NF==7) { $8="dummy" }
         }
        print $0 
       }'  inputfile > tmp.tmp

So the last 2 fields in tmp.tmp can be a real value, or just fiber filler: "dummy", but there will always be 8 fields. The last two fields cannot be blank or bash will not read them into a variable.
 

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