Package Bio :: Package MetaTool
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Package MetaTool

source code

Parser for output from MetaTool 3.5 (DEPRECATED).

MetaTool is a program which defines metabolic routes within networks. This parser does not support the current version, MetaTool 5.0.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed& list_uids=10222413&dopt=Abstract

Submodules [hide private]

Classes [hide private]
  Iterator
Iterator interface to move over a file of MetaTool entries one at a time.
  _RecordConsumer
Create a MetaTool Record object from scanner generated information.
  _Scanner
Start up Martel to do the scanning of the file.
  RecordParser
Parse MetaTool files into Record objects
Functions [hide private]
 
_strip_and_combine(line_list)
Combine multiple lines of content separated by spaces.
source code
Variables [hide private]
  __warningregistry__ = {('Bio.MetalTool was deprecated, as it o...
Function Details [hide private]

_strip_and_combine(line_list)

source code 

Combine multiple lines of content separated by spaces.

This function is used by the EventGenerator callback function to combine multiple lines of information. The lines are first stripped to remove whitepsace, and then combined so they are separated by a space. This is a simple minded way to combine lines, but should work for most cases.


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.MetalTool was deprecated, as it only supported the obsoleteMeta\
Tool 3.5 output.',
  <type 'exceptions.UserWarning'>,
  16): 1}