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
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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.
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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.
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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
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__init__
(self, elem)¶ Initialize the class.
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parse
(self)¶ Parse the input elements.
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