Hi,
That's what I figured out.
1. Version as of August 13.
>>> seqdb.BlastDB('R1')
{}
Less than 1 sec. Returns empty dict.
2. Version as of Today.
>>> seqdb.BlastDB('R1')
<BlastDBbase 'R1'>
Took several minutes and load all indice into memory.
One of our researcher reported this problem about a few months ago, his
worry is pygr is TOO SLOW. We had thought there should be some problem with
the RAID, but later I found out it was seqdb.BlastDB.
Yours,
Namshin Kim
On Mon, Oct 13, 2008 at 1:06 PM, Namshin Kim <[EMAIL PROTECTED]> wrote:
> I tried to open it by bsddb.btopen. It was very fast and didn't require
> any memory prior to actual query. Does it have to do with recent
> BlastDbBase?
>
> x = bsddb.btopen('R1.seqlen')
>
> Yours,
> Namshin Kim
>
> On Mon, Oct 13, 2008 at 12:52 PM, Namshin Kim <[EMAIL PROTECTED]> wrote:
>
>> Hi,
>>
>> I made a seqdb.BlastDB for 30million sequences. My problem is that it
>> requires very long time (more than 5 min) to load that seqdb.BlastDB. I
>> checked memory and found out that it actually load all indice into memory,
>> 30million. Due to this behavior, pygr NLMSA has become very slow NLMSA. Does
>> anybody know how to solve seqdb.BlastDB problem?
>>
>> Thanks,
>> Namshin Kim
>>
>>
>
>
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