in reply to BioPerl StandAloneBlast is returning unexpected undefined SearchIO object

I may be misreading the code (little wonder), but it looks to me that even if you pass a reference to an array or Bio object, the module you're using writes that data to a temporary file in order to pass it to the executable anyway.

From my (limited) perspective, it looks like it might be a whole lot easier to start the executable directly using a piped open and pass the data through yourself. At least you'd know what was going on.

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Re^2: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object
by WonkoTheSane (Novice) on Jun 25, 2009 at 18:08 UTC
    I may be misreading the code (little wonder)
    Huh? is my code that terrible? Or is it because its hard to understand if one is not familiar with BioPerl? Because that I can understand :)

    But your making a good point, even though it still don't explain the error. But I think that it will definitely improve my workaround. Thanks!
[reply]
      Huh? is my code that terrible?

      Not your code (actually I didn't look at it that closely:); I was referring to the code inside Bio::Tools::Run::StandAloneBlast which I find extremely opaque.

      Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
      "Science is about questioning the status quo. Questioning authority".
      In the absence of evidence, opinion is indistinguishable from prejudice.
[reply]

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