[Bioperl-l] seq object usage
Fields, Christopher J
cjfields at illinois.edu
Tue Jun 12 11:31:32 EDT 2012
Bio::Seq::LargePrimarySeq/LargeSeq actually is a better fit here than my previous suggestion; note the 'add_sequence_as_string' method:
On Jun 12, 2012, at 10:26 AM, Christopher Fields wrote:
> Bio::LiveSeq is supposed to handle cases like this:
> ...but it is severely undocumented. This is one we're planning on pulling out of core and releasing on its own. The code hasn't been updated in quite a while, but it's better than starting from scratch if anyone wants to take it.
> On Jun 12, 2012, at 8:54 AM, Roy Chaudhuri wrote:
>> Bio::Seq's seq method just delegates to Bio::PrimarySeq:
>> So this should work:
>> You're right about the memory thing though. Math, couldn't you just print out a Fasta file directly rather than using BioPerl?
>> On 12/06/2012 14:28, Frank Schwach wrote:
>>> 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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>>>> Bioperl-l at lists.open-bio.org
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