Awk conditional filter one file based on another (or other solutions)

Question

Programming beginner here needs some help modifying an AWK script to make it conditional. Alternative non-awk solutions are also very welcome.

NOTE Main

Answer 1

One way.

awk '
    BEGIN { FS = "\t"; }

    ## Save third, fifth and seventh field of first file in arguments (refGene.txt) as the key
    ## to compare later. As value the field to print.
    FNR == NR {
        pair[ $3, $5, $6 ] = $13;
        next;
    }

    ## Set the name of the output file.
    FNR == 1 {
        output_file = "";
        split( ARGV[ARGIND], path, /\// );
        for ( i = 1; i < length( path ); i++ ) {
            current_file = ( output_file ? "/" : "" ) path[i];
        }
        output_file = output_file "/ListOfGenes_" path[i];
    }

    ## If $1 = $3, $2 = $5 and $3 = $6, print $13 to output file.
    {
        if ( pair[ $1, $2, $3 ] ) {
            print pair[ $1, $2, $3 ] >output_file;
        }
    }
' refGene.txt /files/rubal/*.txt