[Biopython-dev] scanner in Bio.Fasta

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Thu Mar 17 00:17:44 EST 2005


There used to be a _Scanner class in Bio.Fasta. It was removed about a 
year ago when Bio.Fasta started using Martel. As a result, the 
fasta_consumer.py example in Doc/examples no longer works (this example 
is also in the tutorial); see also bug 1741.

The goal of the example can be achieved also by loading the Fasta file 
as a dictionary, so there is an easy way to fix this. However, in the 
section "General Parser Design" in the documentation, it says

"""
All of the parsers have two components:

    1. Scanner - The part of the parser that actually does the work or 
going through the file and extracting useful information. This useful 
information is converted into Events.

    2. Consumer - The consumer does the job of processing the useful 
information and spitting it out in a format that the programmer can use. 
The consumer does this by receiving the events created by the scanner.
"""

So is this no longer true? Or was the Fasta _Scanner removed by mistake? 
Anybody knows what's going on here?

--Michiel.


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