[Biopython-dev] Bio.SeqIO.convert function?

Peter biopython at maubp.freeserve.co.uk
Tue Jul 28 13:19:45 UTC 2009

On Tue, Jul 28, 2009 at 1:55 PM, Michiel de Hoon<mjldehoon at yahoo.com> wrote:
>> Of course, if we have bottlenecks in the SeqIO parsing
>> and writing code, it would be worthwhile of course to fix
>> them - rather than writing a special case converter. Maybe
>> to avoid the gradual build up of too many specialised
>> converters, we might ask as a rule of thumb that it be
>> at least three times faster than using parse/write?
> I have no fundamental objection, but we should first try
> to speed up the current GenBank parser and see if the
> specialized converter is still more than three times faster.

I can already in principle make the current GenBank parser
up to four times faster - I was working on this before all the
FASTQ stuff and would hope to see this in Biopython 1.52,

Even with a change like that to speed up feature location
parsing, it would still be faster still to skip the features in
a GenBank or EMBL file completely.


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