[Biopython-dev] test_Cluster.py fails, "nclusters should be positive"

Peter biopython-dev at maubp.freeserve.co.uk
Mon Feb 26 19:59:45 UTC 2007

I just updated my Linux box running Python 2.4.3 to the CVS version of 
BioPython (including building KDTree).

The bad news is that test_Cluster fails (full details below) with
cluster.error: kcluster: nclusters should be positive

The rest of the unit tests look OK except for some untested modules: the 
BioSQL ones, test_GFF, test_Wise and test_psw (the last two fail because 
I do not have dnal installed).

Interesting some of these tests which pass under Linux fail under 
Windows due to differences in floating point display.  We might want to 
fix that at some point...



$ python test_Cluster.py
data = [  34.300,   3.000,   2.000]
mean is  13.100; median is   3.000
data = [   5.000,  10.000,  15.000,  20.000]
mean is  12.500; median is  12.500
data = [   1.000,   2.000,   3.000,   5.000,   7.000,  11.000,  13.000, 
mean is   7.375; median is   6.000
data = [ 100.000,  19.000,   3.000,   1.500,   1.400,   1.000,   1.000, 
mean is  15.988; median is   1.450

Read data1 (correct)
Read data2 (correct)
Refused incorrect matrix data3
Refused incorrect matrix data4
Refused incorrect matrix data5
Refused incorrect matrix data6
Refused incorrect matrix data7
Refused incorrect matrix data8
Refused incorrect matrix data9
Refused incorrect matrix data10

First data set
Traceback (most recent call last):
   File "test_Cluster.py", line 479, in ?
     run_tests(module = "Bio.Cluster")
   File "test_Cluster.py", line 472, in run_tests
   File "test_Cluster.py", line 181, in test_kcluster
     clusterid, error, nfound = kcluster (data1, nclusters=nclusters, 
mask=mask1, weight=weight1, transpose=0, npass=100, method='a', dist='e')
cluster.error: kcluster: nclusters should be positive

More information about the Biopython-dev mailing list