[Bioperl-l] seq object usage
fs5 at sanger.ac.uk
Tue Jun 12 09:28:30 EDT 2012
the Bio::Seq's "seq" method doesn't take an argument to set a new
sequence, so I think you would have to do it like this:
-seq => $bio_seq_obj->seq .$some_addition_seq
but it wouldn't save you any memory because you still have the whole
sequence in memory.
On 12/06/12 11:27, math math wrote:
> consider the following case:
> A seq object's string field (ie the sequence part) needs to be filled
> gradually in a PERL loop. The seq object(s) can be hundreds of millions
> bases long at the end of this loop. The final goal is to write this seq
> object(s) to an output file (in multi-fasta format).
> My question is, how can one append progressively more sequence to a seq
> object (i.e. instead of all at once, to minimize memory), and make sure
> that these get written to a file.
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