[Bioperl-l] Proposal for bio-perl updates: ACE assembly file

Raoul Jean Pierre Bonnal raoul.bonnal at itb.cnr.it
Mon Feb 14 20:31:13 EST 2005


In data 2/14/2005, "Jordan Swanson" <jswanson at iastate.edu> ha scritto:
> For many of our applications, we only
>need to process one contig at a time, not to mention that reading the entire
>assembly at once requires a large amount of memory and/or disc space.
I'm agree with Jordan, because I have his same problem.
If I have understood well the approach of BioPerl, it uses always this
method, for example loading data from a blast output file ( ref. speed
up parsing blast using tabular output ). I'll prefer to read and create
an object one by one, when the amount of data is huge.
I think that will be useful selecting the preferred approach.

What happend if I don't have the resources to load ALL data ? Processing
one object per time I have to worry about the resources needed by that


by RJP

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