[Biopython-dev] Fasta parser

Michiel de Hoon mdehoon at c2b2.columbia.edu
Sat Jul 1 21:47:28 UTC 2006

Hi everybody,

The Biopython shows the following approach to parsing a Fasta file:

 >>> from Bio import Fasta
 >>> parser = Fasta.RecordParser()
 >>> file = open("ls_orchid.fasta")
 >>> iterator = Fasta.Iterator(file, parser)
 >>> cur_record = iterator.next()

But for large Fasta files, it's very slow, compared to file.read(), 
which may be due to going through Martel (I believe the same was true 
for large GenBank files).

So I'm thinking about writing a simple-minded Fasta parser for better 
performance with large files. What I'm wondering about:
1) Is there some advantage that I overlooked of using Martel for parsing 
Fasta files?
2) Why is it necessary to create a parser first and passing it to 
Fasta.Iterator? Are there any cases where Fasta.Iterator uses something 
other than a Fasta.RecordParser?


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