[Bioperl-l] Batch mode in Bio::DB::GenBank

Marc Logghe MarcL at DEVGEN.com
Fri Mar 31 09:45:04 EST 2006


Hi,
It seems that in the current (CVS of last night) Bio::DB::GenBank
implementation it is not at all possible to set the mode to 'batch'
instead of the default 'single'. Devel::StackTrace revealed that the
mode is hardcoded in the Bio::DB::WebDBSeqI::get_Stream_by_id method.
Is that intended ?
The problem is that with single mode, the request is always done with a
GET. In most cases (at least in my hands) when you pass a batch of 500
id's the request fails because of the url getting too long. All goes
well when the method is overridden whereby the mode option is hardcoded
to 'batch' so that a POST is done.
I think there are at least 2 possibilities:
1) change single to batch in Bio::DB::WebDBSeqI::get_Stream_by_id
2) allow the possibility to pass the mode option when get_Stream_by_id
is called using the Bio::DB::GenBank object
Any comments/preferences before I actually commit some edits ?
Regards,
Marc



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