[BioPython] iterative ace parsing

[edeveaud at pasteur.fr]

On Thu, May 26, 2005 at 09:59:48AM -0400, Frank Kauff wrote:
> Hi,
> 
> On Thu, 2005-05-26 at 15:31 +0200, edeveaud at pasteur.fr wrote:
> > 	Hi,
> > 	
> > after reading the doc for Bio.Sequencing.Ace
> > 
> > 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 ??
> > 
> 
> It works fine, in theory. The problem with ace files is, that they are
> not entirely suitable for contg-by-contig parsing, they can contain
> contig-specific information at the very end of the file. So in your
> case, after reading contig no. 174, there might be still some more info
> left in the file about contigs no. 12, 132, and 160. Depending on what
> kind of contigs you have, there might be no info at all or it's just
> irrelevant for your analysis. The phrap manual (you're using phrap to
> create the contigs?) lists the tags that can appear at the end of an ace
> file, so you might want to have a look there and decide whether they are
> important for you or not. If not, iterating voer contigs should just do
> fine. 

thank's for the clarification.

yes indede we use phred/phrarp in order to create the assembly.
and for the analysis we want to perform we don't care about the eventuals tag
set-up by phrap. we just need the contig coverage and the read starts. 

I'll check the iterative way. 

	thank's again

	Eric

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