[Biopython] Memory leak while parse gbk file?
Peter Cock
p.j.a.cock at googlemail.com
Fri Oct 28 11:52:33 UTC 2011
On Fri, Oct 28, 2011 at 12:46 PM, ning luwen
<bioinformaticsing at gmail.com> wrote:
> 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
Which version of Python are you using? Try calling garbage collection,
import gc
from Bio import SeqIO
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()
gc.collect()
I expect that to fix the increasing memory usage. If it does, then
it isn't a memory leak.
Peter
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