Re: [GUSDEV] problems loading data

[Amruta J. <am...@st...>]

> have a version that works for our data.  Can you tell me a bit
> more about your TIGR files.  Is it one big file or many small
> files for individual contigs?  Did it actually load any data?

It's not a TIGR file, it's an NCBI Entrez XML format file.
It is one single file.
No rows have been inserted in the expected tables.
LoadGeneFeatuteFromXML has a method parseFile having comment as parses TIGR
xml. That's why I was concerned whether LGFFXml could parse my NCBI Entrez
XML file.

Amruta



>
> ---- Original message ----
>>Date: Tue, 19 Apr 2005 17:09:50 -0700
>>From: "Amruta Joshi" <am...@st...>
>>Subject: [GUSDEV] problems loading data
>>To: <gus...@li...>
>>
>>   Hi,
>>
>>   I've successfully installed GUS and am trying to
>>   load data into it.
>>   I have downloaded Bordetella bronchiseptica ds-DNA
>>   sequence in XML format from:
>>
> (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&term=nc_002927)
>>
>>   I tried using LoadGeneFeatureFromXML
>>   (v1.878) plugin, but it prints the length of
>>   submitted sequence as 0.
>>   My guess is that the plugin is not able to parse my
>>   xml file.
>>   Is TIGR XML format different from the Genbank XML
>>   file format?
>>   Is there some other plugin that parses xml to load
>>   data?
>>
>>   I tried using GBParser on data downloaded from the
>>   same site in GenBank (.gb) format. That too failed
>>   with the error:
>>    ------------------ entry number 1 -----------------
>>   You have exceeded the maximum number of allowable
>>   objects in memory:
>>    ------------------ entry number 2 -----------------
>>   Can't call method "getAccession" on an undefined
>>   value
>>
>>   The complete command and errors are pasted below for
>>   reference.
>>
>>
>>   thanks,
>>   Amruta
>>