UNIX for Dummies Questions & Answers

Hello,
I am trying to create a matrix of 0's and 1's depending on whether a gene and sample name are found in the same line in a file called results.txt. An example of the results.txt file is (tab-delimited):

Sample1 Gene1 ## Gene2 ##
Sample2 Gene2 ## Gene 4 ##
Sample3 Gene3 ## Gene 6 ##

The matrix should look like this:

Code:

            Sample1  Sample 2    Sample3
Gene1        1               0           0
Gene2        0               1           0
Gene3        0               0           1

where 1 = 'match found for both gene and sample' and 0 for 'no match'.

My code reads in three files: GenesList.txt (gene names), SampleList.txt (Sample names), and the results.txt file. The output matrix should be Matrix.out.

The multiple grep condition on a single line does not seem to be working properly for me, or maybe I have a problem with my If statement??

For the resultant matrix I expect for any row to have both 0's and 1's, but I end up with an entire matrix of only 1's or only 0's. What am I missing from this bash script?

Code:

for Gene in `cat GenesList.txt`; #Read all the genes in the file
do
      echo -n -e $Gene '\t' >> FusionMatrix.out # Echo gene name (designates the row in my table)
        for Sample in `cat SampleList.txt`;
        do
    grep_output= grep $Sample result.txt | grep $Gene

        #if ["$grep_output" == ""] #my first attempt
        if [[ $grep_output ]]; # second attempt
        then echo -n -e "1" '\t' >> Matrix.out
        else echo -n -e "0" '\t' >> Matrix.out
        fi # Value of 1 if gene involved in that sample, else 0
        done

    echo "">> Matrix.out #Move to next line
done

Thanks for any advice!!