[Bioperl-l] query name in xml blast report

[gert thijs]

Hi,

I am parsing blast reports in XML format with bioperl and this works fine 
except from the extraction of the query ID and description line. If I ask for 
the query name ($r->query_name ) and description ($r->query_description), I 
get empty strings and not values that are in the respective fields in the xml 
file.
In the XML file I find the following lines describing my query sequence:
----
  <BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
  <BlastOutput_query-def>AF059581|INCLUSive|gene|47|1504|1|+|.|id SAHH  ; 
number 1  ; query &apos;AF059581 - SAHH&apos;;</BlastOutput_query-def>
  <BlastOutput_query-len>701</BlastOutput_query-len>
----
I guess the value in the 'BlastOutput_query-ID' field is set by the NCBI blast 
server while the value in the 'BlastOutput_query-def' field matches the header 
of my query sequence, but the quotes are changed to &apos;
Has anyone a suggestion on how to get the full description line from the xml 
report?


Gert




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