I am having a problem getting e-values back from hits and subhits of
SequenceDBSearchResults after parsing a file and converting it to biojava objects
using a BlastLikeSearchBuilder. Scores come back okay, but e-values are always NaN
(even after updating to account for the "e-121" formats). Also, there doesn't seem to
be a way to get the sequence length back from a hit (NOT the length of the match
regions, but the length of the whole thing). Any thoughts? I am still using the
ftp-ed library so if any changes were made in CVS I don't have it.
Thanks a lot,
Susan
>>> Keith James <[EMAIL PROTECTED]> 11/15 4:34 AM >>>
>>>>> "Susan" == Susan Glass <[EMAIL PROTECTED]> writes:
Susan> Thanks to David and Keith for help with the BLAST file
Susan> parsing. I have now managed to download the ssbind package
Susan> and run David's demo program. It's a big help. Thanks a
Susan> lot. I did have to alter the BlastLikeSearchBuilder class
Susan> slightly because of a problem with the makeSubHit() method
Susan> throwing an exception when it encountered the float "e-121"
Susan> (instead of 1e-121) in David's sample BLAST output file.
Susan> Easily altered, but I wonder if anyone else had this
Susan> problem.
Ah, yes. Thanks for reporting that. I had fixed it in at least one of
the other builders. I need to add a Blast report which contains this
type of E-value to the tests (e-121... yuck... why can't it be
consistent?!)
I'll patch and test as soon as I can.
--
-= Keith James - [EMAIL PROTECTED] - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK
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