[Biophp-dev] NCBI query interface and results parser...

S Clark biophp-dev@bioinformatics.org
Fri, 27 Jun 2003 18:21:15 -0600

...now work!

If I did it correctly, the new and updated files for this have been updated 
both at bioinformatics.org's and the sourceforge CVS.

Tested and everything.  The "core" extendable XML parser module is now called 
simply "parser_xml.inc.php", and should correctly be working now with either
filehandles or text (or arrays of lines).  The xml parser extension for
the results obtained by the query interface uses it, as do the EUtils
interfaces (which need to be re-tested to make sure they still work with
the updated parser).

The example/test script just takes one of the sequences that I pasted from
testdata and submits it to blastn for matching, and blindly iterates through
the details of the results (Still trying to decide whether to split out the
parsed/organized results into yet another separate object or just put the
interface methods to the results into the parser - e.g. "showAlignment
($matchnumber)" to grab that match's qseq/midline/hseq and return them...

Finishing the core of the Export module and then nucleotide and protein EFetch 
modules next...

Serge - have you made any changes to the core seq.inc.php file since
the last one posted to CVS?

Thanks for the "welcome back"'s!