Hello Namshin and everyone else,
Chris and I talked about the megatest memory-consumption issue
yesterday and we might have found a way of addressing it. Could you
check whether passing checkFirstID=False to the AnnotationDB
constructor helps when the entire megatest is run?
I have just tested this on llpygr using the following code:
from pygr import sqlgraph, seqdb, worldbase
hg18 = worldbase("Bio.Seq.Genome.HUMAN.hg18")
snp_slices = sqlgraph.SQLTableClustered('PYGR_MEGATESTS.pygr_snp126_hg18',
clusterKey = 'clusterKey', maxCache = 0)
snp_db = seqdb.AnnotationDB(snp_slices, hg18, checkFirstID=XXX,
sliceAttrDict = dict(id = 'chromosome', gene_id = 'name', snp_id =
'snp_id', score = 'score', ref_NCBI = 'ref_NCBI', ref_UCSC =
'ref_UCSC', observed = 'observed', molType = 'molType', myClass =
'myClass', myValid = 'myValid', avHet = 'avHet', avHetSE =
'avHetSE', myFunc = 'myFunc', locType = 'locType', myWeight =
'myWeight'))
If XXX is True (the default), the prompt goes away for a few minutes,
with the amount of used memory gradually increasing from about 1.8 to
about 3 GB. If on the other hand XXX is False, the prompt comes back
instantaneously and memory usage hardly changes.
Cheers,
--
MS
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