[BioPython] BLAST parser updates

Jeffrey Chang jchang@SMI.Stanford.EDU
Tue, 21 Dec 1999 21:38:10 -0800 (PST)


[Jeff's documentation about event-oriented parsers]

>    How do you deal with events coming in in the wrong order?  If a piece is
> deleted from a file, for example, a new section could start before an old
> section finishes.
> 
>                                                             Cayte


The scanners I've been writing have been pretty picky about the data
format.  If it sees something unexpected, such as missing lines of data,
it will complain.

It's possible to write more lenient scanners.  This would require that the
consumer be smart enough to know what errors are recoverable, and which
ones it cannot process.

BTW, I've created about 30 BLAST test cases that will give any parser a
run for its money.  I'll make them available via CVS and tarball as well.

Jeff