[Biopython] Memory leak while parse gbk file?
ning luwen
bioinformaticsing at gmail.com
Fri Oct 28 11:46:07 UTC 2011
Hi,
I have tried to parse about 2000+ gbk file using SeqIO.parse to
parse gbk file, but the memory up quickly. ( in my desktop 4g memory,
out memory after a number of iterates, and then try one work station,
memory used as high as 100g+, and continue increasing)
for temp_name in file_names:#file_names: list of path of gbk files.
f=open(temp_name)
for x in SeqIO.parse(f,'genbank'):
print x.name,len(x.features)
f.close()
I guess there may be memory leak while parse gbk flle.
--
regards,
luwen ning
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