[Biopython-dev] [Bug 2361] Test Suite Failures from Martel/Sax with egenix mxTextTools 3.0

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http://bugzilla.open-bio.org/show_bug.cgi?id=2361





------- Comment #10 from biopython-bugzilla at maubp.freeserve.co.uk  2007-09-12 04:57 EST -------
Regarding GEO, your changes look sensible.  I see you have removed
Bio.Geo.RecordParser() and deprecated Bio.Geo.Iterator() to use a parse()
function.  That makes sense given recent Biopython developments.

For the long term, and thinking as a potential end user, something much more
like Sean Davis'  GEOquery package for R/BioConductor would be much nicer.
http://www.warwick.ac.uk/go/peter_cock/r/geo/

Right now, breaking the GEO files at each ^ (caret) line it perhaps a little
too low level.  In particular, in Biopython I would like to be able to take a
GDS file (GEO Dataset), and have it loaded as an annotated matrix of expression
levels (genes as rows, samples as columns) suitable for use with Bio.Cluster

But that is probable best left as a future enhancement bug.

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We still have the Bio.Fasta.Dictionary and Bio.GenBank.Dictionary classes (and
anything else like it) to worry about.  These use Mindy to build a set of
lookup tables as files on disk, allowing keyed like access to records WITHOUT
having all the records in memory.  I'm a bit hazzy on the implementation
details.  I personally don't use them, and its not something currently
supported by Bio.SeqIO either.

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If you replace the KEGG parser then I fear the remaining problems are very
tightly linked to Martel, but also in my opinion not key features of Biopython.

We could try asking on the egenix mailing list to se if they have some examples
of updating python code to work with mxTextTools 3.0 ...


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