[BioPython] Fasta Iterator

[Iddo Friedberg]

Two problems with this:

1) You need to create a parser. Somthing like:

 >>> parser = Fasta.RecordParser()
 >>> file_for_blast = open('m-cold.fasta','r')
Then:

 >>> f_iterator = Fasta.Iterator(file_for_blast,parser)


Sylvain Schüpp wrote:
> Yes, you're right.
> I'm develloping under Windows XP using Python 2.3.4 and BioPython 1.30 
> for Windows.
> 
> And here is my problem :
>  >>> from Bio import Fasta
>  >>> file_for_blast = open('m-cold.fasta','r')


>  >>> f_iterator = Fasta.iterator(file_for_blast)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^




> But in the directory Lib/Bio/Fasta there is a file (something like 
> __init__.py) which contain a class Iterator.
>  

Exactly! But Python is case sensitive, and you wrote Fasta.iterator 
where it should be Fasta.Iterator

Anyhow, you should instantiate RecordParser, and pass it to Fasta.Iterator.

See section 2.4.3 from the tutorial/cookbook. Also, please let me know 
which prt of the T/C you read to do this. I'll check that part for errors.


HTH,

Iddo




-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
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