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.

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.
RIP PCW

In reply to Re: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by BrowserUk
in thread BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane

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