[Biophp-dev] Updates

S Clark biophp-dev@bioinformatics.org
Tue, 3 Jun 2003 01:19:27 -0600

Actually managed to get some work done today - What I've got done will
be going up in CVS tomorrow soon's I test it to make sure I haven't
broken anything obvious.

esearch and esummary web interface and xml results are now properly split
into separate files.

The "generic" xml parser got extended such that it should now handle
text results as well as filehandles (needed for the NCBI BLAST interface)

I THINK I've worked out all the quirks I needed to get around that I noticed
in my earlier NCBI BLAST tests (i.e. when getting XML format results, the
"QBlastInfo" part of the response doesn't exist as it does in text or
HTML format results, got the "send POST query to webserver" part split off
and working through the postbox class, etc. etc.).  Haven't got the actual
XML results parser written yet, but as it's just an extension of the
"generic" XML parser, I don't think that'll take long.

The updates to esearch, esummary, and the generic xml parser should all
be on CVS tomorrow morning (US West Coast time) along with HOPEFULLY a 
functioning NCBI BLAST set of code.

Nico - can you give me some hints as to your planned structure for filetype
modules in the seqIOWrite section?  One of the things I can work on while on
the road are output modules for Phylip and Clustal (for example).  I'd also
like to work up a simplistic "compare the quality of the match between two
aligned sequences" algorithm, just for quick automated "throw out bad matches"
sort of applications.

More tomorrow.  Bed calls.