type file {};

global string blastdb=@arg("blastdb");
global string curdir=@arg("curdir");
global int njobs=@toint(@arg("njobs"));
global string infile=@arg("infile");

# Application functions: split(), blast(), merge(), parse()

app (file flist) split (file seqs, int nfiles)
{
 split @seqs nfiles @strcat(curdir,"/split") stdout=@flist;
}

app (file o) blast (file i)
{
  blastall "-i" @i  "-d" blastdb "-o" @o "-m8" "-p" "blastp";
}

app (file o) merge (file i[])
{
  cat @filenames(i) stdout=@o;
}

app (file o) parse (file i) {
  parse "--file" @i stdout=@o;
}

# Main script

#file   inputseqs     <"input/tiny.fasta">;
file   inputseqs     <single_file_mapper;file=infile>;
file   fastalist     <"split/flist">;

fastalist = split(inputseqs,njobs);
string fastanames[] = readData(fastalist);

file splitseqs[] <array_mapper; files=fastanames>;
file output[]    <simple_mapper; location="output/", suffix=".blastout">;

foreach f, i in splitseqs {
  output[i] = blast(f);
}

file blastout<"output/blast.all.out">;
blastout = merge(output);

file parseout<"output/parse.out">;
parseout = parse(blastout);











/* Notes:

split_fasta.pl input/unknown.fasta 100 input > list_of_files.txt

blastall -i input/fasta_chunk_1 -d $BLASTDB/nr/nr -o output/blast_chunk_1.out -m8 -p blastp

echo "output/blast_chunk_1.out" >> output/blast_output_files.txt

concatenate_files.pl output/blast_output_files.txt output/blast_out.blast

parse_tabbed_blast.pl --file output/blast_out.blast > output/jobResults.txt

*/