New issue 2261: PyPy 5.0.0 very slow when using BioPython BLAST XML parsing
under OS X
https://bitbucket.org/pypy/pypy/issues/2261/pypy-500-very-slow-when-using-biopython
Terry Jones:
I just upgrade from pypy4.0.1 to 5.0.0 (OS X 10.10.5, via brew) and was
surprised to find some code running much slower. I have a simple piece of code
that uses BioPython (which in turrn uses expat to parse some XML). On python
2.7 my code runs in ~9 seconds, in python 3.5 it’s ~10 secs, in pypy 4 it’s 18
seconds, and in pypy 5 it’s 25 seconds.
You can reproduce it by installing BioPython (I have 1.64 in my virtualenv) and
running the following minimal example:
```
#!python
from __future__ import print_function
import sys
from Bio.Blast import NCBIXML
count = 0
with open(sys.argv[1]) as fp:
for record in NCBIXML.parse(fp):
count += 1
print(count)
```
with the attached XML (once uncompressed) file given on the command line.
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