[Bioperl-l] How to read in the whole fasta file in the memory?

[Jason Stajich]

or use a database object so you can retrieve sequences that have a  
particular id. See Bio::DB::Fasta
On Dec 30, 2009, at 10:04 AM, Sean Davis wrote:

> On Wed, Dec 30, 2009 at 12:26 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> With Bio::SeqIO, I can only read in the records in a fasta file one  
>> by
>> one. This is preferable if there are many records in a file.
>>
>> But I also want to read all the records in. I could use a while loop
>> to read all records in. But could somebody let me know if there is a
>> function in bioperl that can read in all the record at once and  
>> return
>> me an object?
>
> In perl, you can use an array to store the records.  You could also
> use a hash if you have reasonable keys for the entries.
>
> Sean
>
>
>> http://www.bioperl.org/wiki/HOWTO:SeqIO
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/