> what is the typical usage pattern of that list?
For me, it's almost always streaming through it, building up some other
data structure as I run along.
> if (memory) space is very tight, then the result of the parse
> could just be a list of file offsets, to be used later,
> when elements are a
Hi,
for mmap-ing, there are xyz-mmap libraries on hackage.
In general, for libraries accessing this kind (huge bio data base) of
data, we want both, efficient streaming and efficient pull-in of the
whole dataset.
Gruss,
Christian
* Johannes Waldmann [27.06.2014 15:58]:
> Hi,
>
> >> what is me
Hi,
>> what is meant by "the parsing is lazy" exactly?
> I don't know, did I use that term?
Yes, in the docs
http://hackage.haskell.org/package/blastxml-0.3.1/docs/Bio-BlastXML.html
>> You want a BlastResult with a lazy list of results
>> (containing BlastRecords with a lazy list of hits, etc)?
> (I'm interested in XML processing as well -
> also large files, though not for bio stuff)
> can you show a test case (actual source code,
> XML input data, and your performance measurements)?
Probably - the data file I used is a bit large (eight gigs), so probably
not ideal to ship around as a
On 06/27/2014 12:31 PM, Ketil Malde wrote:
> performance of the blastxml library,
> which parses Blast XML output files.
(I'm interested in XML processing as well -
also large files, though not for bio stuff)
can you show a test case (actual source code,
XML input data, and your performance mea
One of the issues we've discussed briefly, was the performance of the
blastxml library, which parses Blast XML output files. These files can
typically be large, and there is quite a bit of overhead in parsing
them - which poses a challenge for transalign. It uses Neil Mitchells
'tagsoup' library
Hello!
Here is my blog post for the 6th coding week.
This is what I did the last week: http://biohaskell.org/GSoC_blog/Week_5
And this is my plan for this week:
http://biohaskell.org/GSoC_blog/Weeks_6and7
The last weeks I changed a lot in the code to decrease the time and space
consumption. The a
