[Biopython-dev] Reading sequences: FormatIO, SeqIO, etc

[Michiel de Hoon]

Thanks Peter.

Peter (BioPython Dev) wrote:
> QUESTION: What do you all tend to use?

I use the stuff in Bio.Fasta, but actually just because it's in the 
documentation. From your timings, and also because I'm not smart enough 
to be able to understand Martel, let alone maintain Martel-based 
parsers, I'm pretty much in favor of Bio.SeqIO.

>  Should I draft a "questionnaire" 
> to be posted on the main discussion list (and the announcements?).

By all means, yes. In the questionnaire, be sure to separate the issue 
of parser internals (Martel vs. pure Python) from the issue of how the 
results should be formatted (Fasta.Record or SeqRecord).

--Michiel