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executable file 58 lines (47 sloc) 1.656 kB
import os
import sys
import unittest
from Bio.Sequencing import Phd
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [PhdTestOne]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class PhdTestOne(unittest.TestCase):
def setUp(self):
self.handle = open("Phd/phd1")
def tearDown(self):
self.handle.close()
def t_check_record_parser(self):
"""Test to check that record parser parses all records of a contig.
"""
recparser = Phd.RecordParser()
it = Phd.Iterator(self.handle,recparser)
x=0
print
while 1:
r=it.next()
if not r:
break
x+=1
print '---- Record',x,'----'
print 'Filename:',r.file_name
comments=r.comments.items()
comments.sort()
print '\n'.join([c[0]+': '+str(c[1]) for c in comments])
allsites=['-'.join(s) for s in r.sites]
print allsites[:10],'...',allsites[len(allsites)/2-5:len(allsites)/2+5],'...',allsites[-10:]
print r.seq.tostring()[:10],r.seq.tostring()[-10:]
print r.seq_trimmed.tostring()[:10],r.seq_trimmed.tostring()[-10:]
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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