Issue 111 + 112 uniprot

[HobnobMancer]

Migrate from bioservices.UniProt().get_df() to bioservies.UniProt().mapping():

• minimise crashing from bioservices get_df method
• faster: increased batch sizes
• does not require querying NCBI

[codecov]

Codecov Report

Merging #115 (b902dea) into master (a5da4ea) will decrease coverage by 3.13%.
The diff coverage is 24.97%.

@@            Coverage Diff             @@
##           master     #115      +/-   ##
==========================================
- Coverage   56.22%   53.10%   -3.13%     
==========================================
  Files          61       69       +8     
  Lines        5576     6011     +435     
==========================================
+ Hits         3135     3192      +57     
- Misses       2441     2819     +378     

[HobnobMancer]

New in version 2.3.0

• Downloading protein data from UniProt is several magnitudes faster than before - and should have fewer issues with using older version of bioservices

  • Uses bioservices mapping to map directly from NCBI protein version accession to UniProt
  • cw_get_uniprot_data not longer calls to NCBI and thus no longer requires an email address as a positional argument

• Updated database schema: Changed Genbanks 1--* Uniprots to Genbanks *--1 Uniprots. Uniprots.uniprot_id is now listed in the Genbanks table, instead of listing Genbanks.genbank_id in the Uniprots table

• Retrieve taxonomic classifications from UniProt

  • Use the --taxonomy/-t flag to retrieve the scientific name (genus and species) for proteins of interest
  • Adds downloaded taxonomic information to the UniprotsTaxs table

• Improved clarrification of deleting old records when using cw_get_uniprot_data

  • Separate arguments to delete Genbanks-EC number and Genbanks-PDB accession relationships that are no longer listed in UniProt for those proteins in the local CAZyme database for proteins whom data is downloaded from UniProt
  • New args:
    • --delete_old_ec_relationships = deletes Genbank(protein)-EC number relationships no longer in UniProt
    • --delete_old_ecs = deletes EC numbers in the local db not linked to any proteins
    • --delete_old_pdb_relationships = deletes Genbank(protein)-PDB relationships no longer in UniProt
    • --delete_old_pdbs = deletes PDB accessions in the local db not linked to any proteins

• Retrieve the local db schema

  • New command cw_get_db_schema added.
  • Retrieves the SQLite schema of a local CAZyme database and prints it to the terminal

• Added option to skip retrieving the latest taxonomic classifications NCBI taxonomies

  • By default, when retrieving data from CAZy, cazy_webscraper retrieves the latest taxonomic classifications for proteins listed under multiple tax
  • To increase scrapping time, and to reduce burden on the NCBI-Entrez server, if this data is not needed (e.g. GTDB taxs will be use) this step can be skipped by using the new --skip_ncbi_tax flag.
  • When skipping retrieval of the latest taxa classifications from NCBI, cazy_webscraper will add the first taxa retrieved from CAZy for those proteins listed under multiple taxa

• Update documentation

  • README
  • Read the docs
  • Updated db schema
  • Added db schema to README