Package Bio :: Package KEGG :: Package KGML :: Module KGML_parser
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Module KGML_parser

source code

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:
Functions:
Classes [hide private]
  KGMLParser
Parses a KGML XML Pathway entry into a Pathway object.
Functions [hide private]
 
read(handle, debug=0)
Parse a single KEGG Pathway from given file handle.
source code
 
parse(handle, debug=0)
Return an iterator over Pathway elements.
source code
Variables [hide private]
  __package__ = 'Bio.KEGG.KGML'
Function Details [hide private]

read(handle, debug=0)

source code 

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.

parse(handle, debug=0)

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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.