biopython v1.71.0 Bio.KEGG.KGML.KGML_parser

Classes and functions to parse a KGML pathway map.

The KGML pathway map is parsed into the object structure defined in KGML_Pathway.py in this module.

Classes:

  • KGMLParser - Parses KGML file

Functions:

  • read - Returns a single Pathway object, using KGMLParser internally

Link to this section Summary

Functions

Return an iterator over Pathway elements

Parse a single KEGG Pathway from given file handle

Link to this section Functions

Return an iterator over Pathway elements.

Arguments:

  • handle - file handle to a KGML file for parsing
  • debug - integer for amount of debug information to print

This is a generator for the return of multiple Pathway objects.

Parse a single KEGG Pathway from given file handle.

Returns a single Pathway object. There should be one and only one pathway in each file, but there may well be pathological examples out there.