Welcome to prunito’s documentation!

A package providing tools for accessing and working with protein sequences and associated data. The focus is on data from the UniProtKB. This is reflected in the package name which is an anagram of UniProt. UniProt has two sets of REST services, uniprot.org and the newer Proteins API. Additionally, a few tools for accessing services or working with data from the following resources are provided:

• EuropePMC
• InterPro
• ENA
• EBI web services

Contents:

• Installing prunito
• Dependencies
• Quick start
• Dealing with results from web services
  • What does WSResponse (sub)classes do?
  • Results from searching UniProtKB
  • Results from identifiers mappings
  • Results from HMMER searches
  • Results from searching EuropePMC
  • Taxonomy results
• UniProt REST services
  • UniProt vs. Proteins API
  • Searching UniProtKB
  • Looking at results
  • Mapping identifiers
  • Converting between different UniProt formats
  • Retrieving batches of entries
  • Retrieving taxonomy data
• Parsers for UniProt data
  • UniProtKB text parser
• API for uniprot.org
• UniProt Proteins API
• Utilities used in the package

Indices and tables

• Index
• Module Index
• Search Page