biopython

v1.71.0

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

Functions

__init__()

Initialize the class

_parse_comment()

Parse comments (PRIVATE)

_parse_protein()

Parse protein names (PRIVATE)

parse()

Parse the input

Link to this section Functions

Link to this function __init__()

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:

return_raw_comments=True

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).

Link to this function parse()

Parse the input.