biopython v1.71.0 Bio.SeqIO.UniprotIO.Parser

Parse a UniProt XML entry to a SeqRecord.

return_raw_comments=True to get back the complete comment field in XML format alphabet=Alphabet.ProteinAlphabet() can be modified if needed, default is protein alphabet.

Link to this section Summary


Initialize the class

Parse comments (PRIVATE)

Parse protein names (PRIVATE)

Parse the input

Link to this section Functions

Initialize the class.

Link to this function _parse_comment()

Parse comments (PRIVATE).

Comment fields are very heterogeneus. each type has his own (frequently mutated) schema. To store all the contained data, more complex data structures are needed, such as annotated dictionaries. This is left to end user, by optionally setting:


The original XML is returned in the annotation fields.

Available comment types at december 2009:

  • “allergen”
  • “alternative products”
  • “biotechnology”
  • “biophysicochemical properties”
  • “catalytic activity”
  • “caution”
  • “cofactor”
  • “developmental stage”
  • “disease”
  • “domain”
  • “disruption phenotype”
  • “enzyme regulation”
  • “function”
  • “induction”
  • “miscellaneous”
  • “pathway”
  • “pharmaceutical”
  • “polymorphism”
  • “PTM”
  • “RNA editing”
  • “similarity”
  • “subcellular location”
  • “sequence caution”
  • “subunit”
  • “tissue specificity”
  • “toxic dose”
  • “online information”
  • “mass spectrometry”
  • “interaction”
Link to this function _parse_protein()

Parse protein names (PRIVATE).

Parse the input.