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)

[download]

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...

Excellence is an Endeavor of Persistence. Chance Favors a Prepared Mind.

In reply to Re: [BioPerl] a warning I do not understand omits a sequence by biohisham
in thread [BioPerl] a warning I do not understand omits a sequence by Anonymous Monk

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