Changed file conversion capabilities to a module

MasterFASTA parses user input as before but now passes the data to a
very generic module that takes the arguments in_file and out_file. These
two arguments correspond to the file to convert from and the file to
convert to respectively. The module prints a custom error message
listing compatible file types if an incompatible file type is given. The
module was modified to appropriately deal with files named such things
as this.is.a.file.txt. Finally, the GFF import was made optional since
not everyone wishes to write GFF files and not everyone has BCBio
installed.