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Module: __init__ Bio/KEGG/Map/__init__.py

KEGG Map package

This module provides code to import KEGG Pathway maps for use with the Biopython Pathway module.

The pathway maps are in the format:

RXXXXX:[X.X.X.X:] A + 2 B <=> C RXXXXX:[X.X.X.X:] 3C <=> 2 D + E ...

where RXXXXX is a five-digit reaction id, and X.X.X.X is the optional EC number of the enzyme that catalyze the reaction.

Classes: Iterator -- Iterates through a file of map file. Parser -- Parses KEGG map lines into Pathway.Reaction objects.

_Scanner _Consumer

Imported modules   
from Bio import File
from Bio.ParserSupport import AbstractConsumer, EventGenerator
from Bio.Pathway import Reaction
import Martel
from Martel import RecordReader
import map_format
from xml.sax import handler
Classes   
Iterator

Iterator to read a file of KEGG reactions one at a time.

Parser

Parse KEGG Map files into Pathway.Reaction objects

_Consumer

Create a Pathway.Reaction object from scanner events.

_Scanner

Start up Martel to do the scanning of the file.

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