Re: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object

It appears that the code

$blast_report->next_result();
[download]

is returning undef instead of a blessed object. Is that object (StandAloneBlast) your code? Maybe it has error reporting options, or is supposed to return undef sometimes...?

Comment on Re: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object Download Code

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Re^2: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane (Novice) on Jun 25, 2009 at 17:06 UTC
StandAloneBlast is a module in BioPerl (www.bioperl.org) and therefore kind of a black box.. With that said, it should only return undef if the blast search that it did returns empty handed. But from doing the blast search manually (in my workaround) it can be seen that the search is not empty.	[reply]
Re^3: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by John M. Dlugosz (Monsignor) on Jun 25, 2009 at 17:24 UTC
Than it indicates a bug in that module. (That could be a documentation bug if its just not matching what you did by hand)	[reply]
Re^4: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane (Novice) on Jun 25, 2009 at 18:13 UTC
This is also what I'm thinking. Only thing is that I think it is a widely used module and it would seem odd to me that no one has encountered this bug before :)	[reply]