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Update to the retrieve functionalities

Jonkheer, Eef requested to merge update_retrieve_features into master

The functionalities of retrieve_genomes and retrieve_regions were somewhat redundant. Therefore, I integrated the option to retrieve complete genomes into retrieve_regions.

For retrieve_features it is now possible to select genomes with --skip or --reference in addition to using a file with--genome-numbers.

Proper error handling was added to all both functions.

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