Create UniProt Mapping file.

[nairod2000]

Corrected spelling error in generate_tsvs.rb, created tsv generator and presenter, scheduled the task to run monthly, added functions to get uniprot names and created the uniprotmapping tsv. Need help getting the correct counts for variants and evidence items that are non-rejected.

[acoffman]

Made some comments based on what we talked about on the call - let me know if you have any questions!

[acoffman]

You probably don't need the indirection here of calling e.objects and can delete def self.objects in the presenter file. This can probably just be Gene.find_each

[acoffman]

I might change this to be e.rows_from_object() and assume you always get back an Array of rows and push the logic of handling multiple (or no) uniprot ids down a level. (See other comment)

[acoffman]

I'd rename to rows_from_object() and do something along these lines (haven't tested it, just off the top of my head):

swissprot_names = Array(Scrapers::MyGeneInfo.get_swissprot_name(gene))
formatted_overview = formatted_overview_col(gene)
swisprot_names.map do |swissprot_name|
  if name == 'N/A'
    nil
  else 
    [gene.name, swissprot_name, formatted_overview]
  end
end.compact

That way you have a list of rows for your TSV, compact will remove the nils and the code that actually writes the TSV can just be a simple iteration over genes, calling this, and then writing a row for each item this returns.

[acoffman]

I'd get the counts in the following ways:

eid_count = EvidenceItem.joins(variant: [:gene]).where("evidence_items.status != 'rejected'").where(variant: {gene: gene}).distinct.count
variant_count = gene.variants.joins(:evidence_items).where("evidence_items.status != 'rejected'").distinct.count
assertion_count = gene.assertions.where("status != 'rejected'").distinct.count

You could also invert the logic and do something like this:

Assertion.joins(:gene).where("status != 'rejected'").where(gene: g).distinct.count

depending on what's more clear to you.