[Biopython-dev] [Bug 2778] New: Efficiency improvement in function Bio.SeqUtils.GC()

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2778

           Summary: Efficiency improvement in function Bio.SeqUtils.GC()
           Product: Biopython
           Version: 1.48
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P5
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: wscott at chem.ubc.ca


Bio.SeqUtils.GC recalculates the gc variable in a loop using a dictionary
whereas it could simply be calculated after the loop.
The following code is suggested to replace the function:

def ScoGC(seq):
   """ calculates G+C content """
   gc=sum(map(seq.count,['G','C','g','c','S','s']))
   return gc*100.0/len(seq)


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.