Changed output directory option and added overwrite option

[guignonv]

By default, SHOOT outputs a serie of files in the same directory as the input FASTA file. This PR changes that behavior so output files are by default put into a "input_file_path.shoot" directory instead. It is possible to change the default output directory to a specified one using the new "-d " option (or "--ouput_directory ").
It is therefore possible to check for previous computation and abort to prevent overwriting. To force overwriting, a new option has been added: "--overwrite".

[guignonv]

Note: to keep the same behavior as before (ie. all outputs in the same directory as the input fasta), just change the command line:

• from old cmd:
  python shoot /data/dir/test.fa /data/shootdb
• to new cmd:
  python shoot --overwrite -d /data/dir /data/dir/test.fa /data/shootdb