Light refactoring of database management patch

[sdhutchins]

Changes

• Changed module BioSQL to biosql

One issue I was having is that BioSQL was not being imported properly from biopython since our package has a BioSQL. I changed it to biosql in our package.

• Added check_ingredients function. We were reusing a lot of code so this should cut down on that a bit and give us some reproducibility.

    def _check_ingredients(self, cookie, path, no_input, extra_context):
        """Check if a directory exists. If not, create it."""
        if self.cookie_jar:
            if self.exists(str(path)):
                os.chmod(str(path), mode=0o777)
                self.cookielog.warning('%s already exists. ✔' % str(path))

        else:
            cookiecutter(str(cookie), no_input=no_input,
                            extra_context=extra_context, 
                            output_dir=str(self.cookie_jar))
            os.chmod(str(path), mode=0o777)
            self.cookielog.info('%s was created. ✔' % str(path))

[sdhutchins]

This is still in progress.

[sdhutchins]

@grabear This should be ready!