[Biodevelopers] (#=#) XML for huge DB? - XML::Parser....

[Joe Landman]

Hi Dan:

 Can you create a small example set of BLAST output, and a small version
of the test code (just pull out the troublesome stuff) and share it?

 Barring that, if it is not possible, try using Data::Dumper on the
resulting parsed document.  Could you turn on the ErrorContext expat
option (in XML::Parser)?  Reading the rest of the man page, if you are
using it in streaming mode, look carefully at the Stream_Delimiter
option.

Joe

On Fri, 2003-08-01 at 13:33, Dan Bolser wrote:
> I am now deeply frustrated. 
> 
> My XML::Parser is working almost perfectly, apart from
> dumping the occasional Q instead of the correct 
> Hit_accession, and then somtimes 'loosing' the last
> digit of the Hsp_num...
> 
> I only notice these when they violate my primary
> keys, so I don't know how many 'silent' mutations
> are being introduced.  
> 
> If I put some new lines in the file, after the <!DOCYTPE,
> and before <BlastOutput, other characters go missing,
> but the previous ones are returned. There is a specific
> number of lines which gives no detected mutations, 
> 
> but puting the file back the way it was makes the original
> problem come right back - in exactly the same predetermined
> way....
> 
> Who should I kill?
> 
> Please don't sugest using another parser...
> 
> Which Bioperl should I use?
> 
> I found the great looking 
> 
> BLAST::Report
> 
> http://ccgb.umn.edu/~crow/projects/xmlblast/
> 
> uses dom, which is a shame. 
> 
> Thanks anyone who can return my missing characters,
> and my sanity....
> 
> Why would XML::Parser develope this problem is such
> a derministic random way?
> 
> ?Thanks again, Dan.
> 
> 
> 
> _______________________________________________
> Biodevelopers mailing list
> Biodevelopers at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biodevelopers
-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615