Draft python API based on uses cases

[christiam]

Create a draft python API based on virus discovery 2 group use cases that would facilitate access to the index

[joanmarticarreras]

Example queries to BigQuery:

• [ ] GET Viral TaxID BY CDD
• [ ] GET Viral TaxID BY Host TaxID
• [ ] GET Host TaxID BY Viral TaxID
• [ ] GET GenBank accession number BY Viral TaxID
• [ ] GET Viral Graph BY CDD
• [ ] GET Viral Graph BY Viral TaxID
• [ ] GET Viral TaxID BY Viral Species Name NOTE This can be troublesome

[sejmodha]

DRAFT

Operations supported

• function: get_phage_metadata(virus_taxid)

  • input: taxid from virus (integer)
  • output: metadata = tRNA sites?, CRISPR ?

• function name: get_viruses_for_host_taxonomy(taxid)

  • input: taxonomy ID for the host (integer)
  • output: virus_name (list of strings)

• function name: get_host_from_virus_taxonomy

  • description: Gets the hosts that can be infected for a given virus taxonomy ID
  • input: virus taxonomy ID (integer)
  • output: list of possible host_name (list of strings)

• function name: get_virus_host_interactions_from_confidence_level

  • description: Gets the virus-host interactions for given confidence level
  • input: confidence_level
  • output: virus_taxid, host_taxid

• function name: get_SRAs_where_CDD_is_found(cdd_id)

  • input: CDD ID (String) - only viral ones for now.
  • output: SRA ID (list of strings)

• function name: get_domains (FUTURE work)

  • input: virus_taxid
  • output: HMM domains, score, possibly, from David's group: CDDs, locations?

• function name: virus_graph(virus_taxonomy_id)

  • input: virus_taxonomy_id
  • output: if exists, a VCF file that represents the graph ~QUESTION: where is the unpublished/non-genbank data? What's the input if not in genbank?~
  • Can we have a database of graphs, on top of which we could map models to?

[joanmarticarreras]

• function name: get_SRA_runs_that_contain_a_virus

  input: virus_taxid (integer)
  output: SRA list (list of strings)

• function name: get_all_viruses_from_SRA

  input: SRA (string)
  output: virus_taxid (list of integers)

• function name: get_metadata_SRA

  input: value metadata_field
  output: SRA list if true

[christiam]

• function name: get_SRA_runs_that_contain_a_virus

  input: virus_taxid (integer)
  output: SRA list (list of strings)

• function name: get_all_viruses_from_SRA

  input: SRA (string)
  output: virus_taxid (list of integers)

• function name: get_metadata_SRA

  input: value metadata_field
  output: SRA list if true

Per discussion with @sejmodha , this is from data in the previous codeathon, so we'll leave it out for now.

[sejmodha]

CRISPR spacer database

• function: get_spacer_seqs

  • description: Get all spacers for a given (bacterial or archaeal) taxonomy IDs
  • input: taxonomy_id
  • output: spacer_seq(s)

• function: get_organism_from_spacer_seqs

  • description: Get all organisms (bacteria or viral) taxonomy IDs where input spacer sequence is found
  • input: spacer_seq
  • output: taxonomy_id_list