[Bioperl-l] Sorting BLAST hits by score

[Dave Messina]

Hi Lorenzo,



> However, I get the following error message:
> Use of uninitialized value in numeric comparison (<=>) at
> /Library/Perl//5.10.0/Bio/Search/Result/ResultI.pm line 202, <GEN1> line
> 2773.
>

Hmm, I'm not seeing this error message. Could you provide us with your blast
-m8 output so I can test with the same data?


Furthermore, every iteration through the hsps returns the warnig message:
>
> --------------------- WARNING ---------------------
> MSG: Did not define the number of conserved matches in the HSP; assuming
> conserved == identical (152)
>

This is due to the fact that the blast -m8 tabular output doesn't report
conserved matches.

You should be able to suppress these warnings by adding

      -verbose => -1

to your Bio::SearchIO->new parameters, but it isn't working for me for some
reason. Hmm. Anyway, as it's just a warning, it won't affect your results.



Dave