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import sys
import unittest
from ost import *
from ost import settings
from ost.bindings import kclust
class TestkClustBindings(unittest.TestCase):
def testkClustExec(self):
seq_list=io.LoadSequenceList('testfiles/multiple.fasta')
clusters40=kclust.kClust(seq_list,clustering_thresh=40)
clusters90=kclust.kClust(seq_list,clustering_thresh=90)
self.assertEqual(len(clusters40),16)
self.assertEqual(len(clusters90),27)
def testkClustParseOutput(self):
representative_ids=['Q5KTS5.1','P46331.2','P66776.1','P42317.2','P50199.1',
'Q59787.1','Q9WYG0.1','P50197.1','P50198.1','Q7Z4W1.2',
'Q04520.1']
cluster_sizes=[3,3,4,1,7,3,2,1,1,3,1]
result=kclust._ParseOutput('testfiles')
self.assertEqual(len(result),11)
for c, r_id in zip(result, representative_ids):
self.assertEqual(c.representative_id, r_id)
for c, s in zip(result, cluster_sizes):
self.assertEqual(len(c.sequences),s)
if __name__ == "__main__":
# test if kClust is available on system, otherwise ignore tests
try:
blastpath=settings.Locate(('kClust'))
except(settings.FileNotFound):
print("Could not find kClust executable: ignoring unit tests")
sys.exit(0)
from ost import testutils
testutils.RunTests()
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