Re: [Gusdev-gusdev] uploading P. falciparum data

[Thomas O. <ot...@fi...>]

Hi,

I do not know, if that help's, but I had this line,
VLD     CBIL::Bio::GenBank::Origin      1
also like in an endless loop, when I transformed files to Genbank-files=20
with the bioperl-tool.

A part of this, the GBParser seems to need a lot of memory, because for=20
each feature it instance a new class, with a lot of childs, and not all=20
are closed.

Cheers,
Thomas

Steve Fischer wrote:

> i have never run the GBParser.    The plasmoDB folks have used it to=20
> load data.
>
> the funny thing is that P. falciparum is much smaller than human.
>
> unfortunately the guy who know this coded best, Angel, is in europe=20
> this week.
>
> maybe somebody else i'll pick this up.
>
> steve
>
> Fidel Salas wrote:
>
>> I tried uploding P. falciparum chromosome data using the GBParser and
>> ran out of memory in all cases.  setMaximumNumberOfObjects is set to
>> 4000000.  The verbose output files contain the line:
>> VLD     CBIL::Bio::GenBank::Origin      1
>> more than 20 million times before an =A8out of memory=A8 message is
>> output.
>>
>> Here are some of some of the numbers for some of the files:
>> bash-2.05$ grep VLD NC_004325.gbk-gbparser.out | grep -c Origin
>> 20479965
>> bash-2.05$ grep VLD NC_004314.gbk-gbparser.out | grep -c Origin
>> 20356504
>> bash-2.05$ grep VLD NC_004315.gbk-gbparser.out | grep -c Origin
>> 20335688
>>
>> Has anyone run into something similar before?  How did the people
>> working on P. falciparum upload the data into GUS?
>>
>> Thanks
>>
>> Fidel
>>
>>
>>
>>
>>
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