[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



More information about the Biopython mailing list