[Biopython-dev] [Bug 2778] Efficiency improvement in function Bio.SeqUtils.GC()
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Thu Mar 5 10:56:39 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2778
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |RESOLVED
Resolution| |FIXED
------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk 2009-03-05 05:56 EST -------
I've checked that in, but with the existing code to catch a zero length
sequence and return 0 instead of raising a ZeroDivisionError.
def GC(seq):
"""Calculates G+C content, ..."""
gc=sum(map(seq.count,['G','C','g','c','S','s']))
if gc == 0: return 0
return gc*100.0/len(seq)
The old code had been modified several times - it originally calculated the GC%
as the CG count divided by the ATCG count, thus it had to count all the bases.
You are right, this is much cleaner.
Thanks.
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