[BioPython] Memory problems with eutils.efetch_using_dbids ...
BONIS SANZ, JULIO
JBonis at imim.es
Mon Dec 13 09:36:45 EST 2004
I have tried the following code (see at the end).
It is a function that retrieves information about a given SNP from pubmed.
I use:
snpInfoFile = eutils.efetch_using_dbids(...)
and then:
snpInfoFile.readline()
and store this in a list (local memory).
My problem is that I do it for several SNPs and each time some <urllib2.OpenerDirector instance at 0x01435F30> is stored in the RAM. At the end the system hungs up.
Do you know how to free this memory?
I have tried to snpInfoFile.close() and del snpInfoFile but seems not to work!!!!
Help please!!!!!
Regards,
Julio Bonis Sanz
def getSNPInfo(self,rs): #
"""
given a rs return the contig and the position in it
"""
eutils = self.GenBank.EUtils.ThinClient.ThinClient()
snpdbi = self.GenBank.DBIds("snp",[str(rs)])
#print "getSNPInfo(" + str(rs) + ")" + ": " + str(len(gc.garbage))
snpInfoFile = eutils.efetch_using_dbids(snpdbi,rettype = 'flt',retmode = 'html')
del eutils
del snpdbi
snpInfoLines = []
while 1:
cLine = snpInfoFile.readline()
if (cLine == ''):
break
else:
snpInfoLines.append(cLine)
snpInfoFile.close()
del snpInfoFile
print "getSNPInfo(" + str(rs) + ")" + ": " + str(len(gc.garbage))
return snpInfoLines
More information about the BioPython
mailing list