in reply to [BioPerl] a warning I do not understand omits a sequence

Can you show more code and the modules associated then clearly describe the warnings that are returned?

the add_seq method of Bio::SimpleALign would return nothing and it adds just another sequence to the alignment.

what is "$name" intended to hold and how was it initialized?

if you really intended "_seq" as a method that's not how you do it. because "_seq" would be a sub that waits for appropriate argument to be passed 

$self->_seq($new_seq_name)

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Check Bio::CorbaServer::PrimarySeq for an example.

Confusion sets in because _seq can be a hash key too as the OP showed and as is observed in other modules from BioPerl, so seeing more of the code can give clearer clues to what's going on...

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Re: [BioPerl] a warning I do not understand omits a sequence
by Anonymous Monk on Jan 12, 2010 at 09:36 UTC
    Dear Monks,

    Thanks for all your explanations. I think the answer is as simple as Ikegami and BioLion state it: it is likely that there are two sequences with the same name. I shall check this before I try any more complicated solutions.

    @ BioLion: verbose lives in Bio::Root::Root. I am not using it, the default level works for me.
    @ Khen1950fx: I did find the PrimarySeq _seq method, but that only lives in the Corba version and I only use the bio-perl-live packages.

    You have all been very helpful!
    Wil
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