Download RefSeq Genomes and associated Taxonomy

[mikerobeson]

Provide the ability for users to download RefSeq Genome Assemblies, along with their associated taxonomy. See this forum thread for more details.

Some notes:

• In order to obtain the taxonomy,
  • we must pull the accession from the FASTA header of the given assembly.
  • Or parse the Taxonomy ID from the HTML / XML of the returned Assembly Record.
• Can not obtain the taxonomy based on assembly identifiers, i.e. GCF_000213215.
• The goal would bbe to support the following example query against the "Assembly" db, to download all Archaeal and Bacterial Genomes: (txid2[orgn] OR txid2157[orgn]) AND "latest_refseq"[Properties]

[misialq]

I think this can also be achieved by using the NCBI Datasets (see #96), which I started working on a while ago (https://github.com/misialq/RESCRIPt/blob/ncbi-datasets/rescript/ncbi_datasets.py) - using a taxon ID as a query one can pull all assembled genomes, together with their metadata and taxonomies (all using the Datasets API, so no need to do much additional parsing as far as I remember)... Although, it does require some new semantic types defined in https://github.com/bokulich-lab/q2-types-genomics (for storing the genome annotations).

[nbokulich]

@misialq is this PR closed by #153 ?

[misialq]

Yes, it is!