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

[Patrick McConnell]

You will have to post your SAX handler code for us to be any help, I think.

Perhaps your parser is returning character data in separate chunks so that
you are getting events like this:
      (1) Element start: hsp_num
      (2) Characters: 1
      (3) Characters: 2
      (4) Element end: hsp_num
In this case, your hsp num is supposed to be 12, but gets split because the
character buffer was filled at this random time.  I think such an occurance
is legal for a SAX parser, but I am no expert.

I don't know about getting a Q instead of the proper accession.

Good luck!

-Patrick





Dan Bolser <dmb at mrc-dunn.cam.ac.uk>@bioinformatics.org on 08/01/2003
01:33:37 PM

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


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.



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