//it is incomplete and might not compile; need to cjeck the data structures

type file;

type aux {
  file faa;
  file phr;
  file pin;
  file psq;
};

aux file_array[];

(file phr, file pin, file psq) formatdb (file input) {
  app {
    formatdb "-i" @input;
  }
}

(file output) blast(file input1, file phr1, file pin1, file psq1, file input2, file phr2, file pin2, file psq2)
{
   app{
     blastall "-p" "blastp" "-d" @input1 "-i" @input2 "-m" "9" "-o" @output;
   } 
}

(file output) reciprocal(file reciprocalScript, file input1, file input2) {
  app {
    perl @reciprocalScript  "-i1" @input1 "-i2" @input2 "-o" @output;
  }
}


file FASTA_files[] <filesys_mapper; location="../FASTA", suffix=".faa">;

file reciprocalScript <"simple_reciprocal_best_hits.01b.pl">;


foreach f, i in FASTA_files {

   file_array[i].faa = f;
   file_array[i].phr = <single_file_mapper; file=@strcat(f,".phr")>; 
   file_array[i].pin = <single_file_mapper; file=@strcat(f,".pin")>;
   file_array[i].psq = <single_file_mapper; file=@strcat(f,".psq")>;
   (f.phr, f.pin, f.psq) = formatdb(f.faa); //constructs the auxiliary files needed in blast step
}


foreach i, i_index in file_array {
   foreach j, j_index in file_array  {

        file output1 = <single_file_mapper; file=@strcat("out",@(i.faa),"2",@(j.faa),".txt")>;
        output1 = blast(i.faa, i.phr, i,pin, i.psq, j.faa, j.phr, j.pin, j.psq);

        file output2 = <single_file_mapper; file=@strcat("out",@(j.faa,)"2",@(i.faa),".txt")>;
  	// output2 = blast(a[j],a[i]); would be desired to call it this way ...
        output2 = blast(j.faa, j.phr, j.pin, j.psq, i.faa, i.phr, i.pin, i.psq);

        file output = <single_file_mapper; file=@strcat("ortholog.pairs.",@(i.faa),"-",@(j.faa),".txt")>;
        output = reciprocal(reciprocalScript, output1, output2);
   }
}