[Biopython-dev] [Bug 2790] New: Genepop parser creates a full representation of the file on memory
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Tue Mar 17 00:40:01 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2790
Summary: Genepop parser creates a full representation of the file
on memory
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: PopGen
AssignedTo: biopython-dev at biopython.org
ReportedBy: tiagoantao at gmail.com
The genepop parser creates a full representation of the file on memory.
This is fine for most users (like with 100/200 individuals and 100 markers)
but, more and more people appear now with thousands of individuals and/or
thousands of loci. In some cases the whole file doesn't fit memory.
An alternative (iterator based) interface has to be created which only
maintains a subset of the file in memory
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