[BioPython] iterative ace parsing

edeveaud at pasteur.fr edeveaud at pasteur.fr
Thu May 26 09:31:53 EDT 2005


	Hi,
	
after reading the doc for Bio.Sequencing.Ace

I would like to run some analysis on an assembly composed of 174 contigs 
based on approximatively 49000 reads.

the only problem is that parsing whole ace file at once needs 872M of memory.

my idea was to itereate over the contigs in order to decrease the memory needs,
but the doc claims 
 2) *** DEPRECATED: not entirely suitable for ACE files! 
             Or you can iterate over the contigs of an ace file one by one in
			 the ususal way:        
			  
could someone point me to some explanation about this warning ??

is the ace parser suitable for iterative tasks ??

	thank's

-- 
>       dvips -o $@ $<     
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partout :))
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