Bio.KEGG.KGML.KGML_parser module
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
- Bio.KEGG.KGML.KGML_parser.read(handle)
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.
- Bio.KEGG.KGML.KGML_parser.parse(handle)
Return an iterator over Pathway elements.
- Arguments:
handle - file handle to a KGML file for parsing, or a KGML string
This is a generator for the return of multiple Pathway objects.
- class Bio.KEGG.KGML.KGML_parser.KGMLParser(elem)
Bases:
object
Parses a KGML XML Pathway entry into a Pathway object.
Example: Read and parse large metabolism file
>>> from Bio.KEGG.KGML.KGML_parser import read >>> pathway = read(open('KEGG/ko01100.xml', 'r')) >>> print(len(pathway.entries)) 3628 >>> print(len(pathway.reactions)) 1672 >>> print(len(pathway.maps)) 149
>>> pathway = read(open('KEGG/ko00010.xml', 'r')) >>> print(pathway) Pathway: Glycolysis / Gluconeogenesis KEGG ID: path:ko00010 Image file: http://www.kegg.jp/kegg/pathway/ko/ko00010.png Organism: ko Entries: 99 Entry types: ortholog: 61 compound: 31 map: 7
- __init__(elem)
Initialize the class.
- parse()
Parse the input elements.