[emboss-dev] Mapping feature types to Sequence Ontology (SO)

Peter Rice pmr at ebi.ac.uk
Wed Aug 17 16:14:15 UTC 2011

On 17/08/2011 17:07, Peter Cock wrote:
> On Wed, Aug 17, 2011 at 4:55 PM, Peter Rice<pmr at ebi.ac.uk>  wrote:
>> If we are reading as sequence input, we need to read all the sequeces
>> into memory and then go back to read the features. For streamed input
>> we can buffer to make the rewind work.
> I'm curious what other file formats needed this kind of work. But it
> is good that you've already got some buffer/cache infrastructure
> in place. Does it boil down to writing temp files in /tmp ?

MSF (checksum at the top), Phylip (number of sequences at the top).

In ajseqwrite.c these are the ones with the Save attribute set true.

We keep them in memory and write them when the output file is closed.


Peter Rice

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