pair_align/tests/run_tests.py

54     for fname in ['1aab', '1ad2', '2trx']:
57             redir_stdout=ph.outFile('%s.stdout' % fname),
58             args=['-s', ph.inFile('%s.fa' % fname),
59                   '-o', ph.outFile('%s.fa' % fname)],
60             to_diff=[(ph.inFile('%s_out.fa' % fname),
61                       ph.outFile('%s.fa' % fname)),
62                      (ph.inFile('%s.stdout' % fname),
63                       ph.outFile('%s.stdout' % fname))])
67     for fname in ['1aab', '1ad2', '2trx']:
71                   '-s', ph.inFile('%s.fa' % fname),
72                   '-o', ph.outFile('%s.protein.fa' % fname)],
73             redir_stdout=ph.outFile('%s.protein.stdout' % fname),
74             to_diff=[(ph.inFile('%s.protein_out.fa' % fname),
75                       ph.outFile('%s.protein.fa' % fname)),
76                      (ph.inFile('%s.protein.stdout' % fname),
77                       ph.outFile('%s.protein.stdout' % fname))])
81     for fname in ['1aab', '1ad2', '2trx']:
85                 redir_stdout=ph.outFile('%s.m%s.stdout' % (fname, m)),
87                       '-s', ph.inFile('%s.fa' % fname),
88                       '-o', ph.outFile('%s.m%s.fa' % (fname, m))],
89                 to_diff=[(ph.inFile('%s.m%s_out.fa' % (fname, m)),
90                           ph.outFile('%s.m%s.fa' % (fname, m))),
91                          (ph.inFile('%s.m%s.stdout' % (fname, m)),
92                           ph.outFile('%s.m%s.stdout' % (fname, m)))])
96     for fname in ['1aab', '1ad2', '2trx']:
99             redir_stdout=ph.outFile('%s.g-20.stdout' % fname),
101                   '-s', ph.inFile('%s.fa' % fname),
102                   '-o', ph.outFile('%s.g-20.fa' % fname)],
103             to_diff=[(ph.inFile('%s.g-20_out.fa' % fname),
104                       ph.outFile('%s.g-20.fa' % fname)),
105                      (ph.inFile('%s.g-20.stdout' % fname),
106                       ph.outFile('%s.g-20.stdout' % fname))])
110             redir_stdout=ph.outFile('%s.e-5.stdout' % fname),
112                   '-s', ph.inFile('%s.fa' % fname),
113                   '-o', ph.outFile('%s.e-5.fa' % fname)],
114             to_diff=[(ph.inFile('%s.e-5_out.fa' % fname),
115                       ph.outFile('%s.e-5.fa' % fname)),
116                      (ph.inFile('%s.e-5.stdout' % fname),
117                       ph.outFile('%s.e-5.stdout' % fname))])
121             redir_stdout=ph.outFile('%s.ms10.stdout' % fname),
123                   '-s', ph.inFile('%s.fa' % fname),
124                   '-o', ph.outFile('%s.ms10.fa' % fname)],
125             to_diff=[(ph.inFile('%s.ms10_out.fa' % fname),
126                       ph.outFile('%s.ms10.fa' % fname)),
127                      (ph.inFile('%s.ms10.stdout' % fname),
128                       ph.outFile('%s.ms10.stdout' % fname))])
132             redir_stdout=ph.outFile('%s.mm-8.stdout' % fname),
134                   '-s', ph.inFile('%s.fa' % fname),
135                   '-o', ph.outFile('%s.mm-8.fa' % fname)],
136             to_diff=[(ph.inFile('%s.mm-8_out.fa' % fname),
137                       ph.outFile('%s.mm-8.fa' % fname)),
138                      (ph.inFile('%s.mm-8.stdout' % fname),
139                       ph.outFile('%s.mm-8.stdout' % fname))])
143     for fname in ['1aab', '1ad2', '2trx']:
146             redir_stdout=ph.outFile('%s.maVTML200.stdout' % fname),
148                   '-s', ph.inFile('%s.fa' % fname),
149                   '-o', ph.outFile('%s.maVTML200.fa' % fname)],
150             to_diff=[(ph.inFile('%s.maVTML200_out.fa' % fname),
151                       ph.outFile('%s.maVTML200.fa' % fname)),
152                      (ph.inFile('%s.maVTML200.stdout' % fname),
153                       ph.outFile('%s.maVTML200.stdout' % fname))])
157     for fname in ['1aab', '1ad2', '2trx']:
160             redir_stdout=ph.outFile('%s.lo5.stdout' % fname),
162                   '-s', ph.inFile('%s.fa' % fname),
163                   '-o', ph.outFile('%s.lo5.fa' % fname)],
164             to_diff=[(ph.inFile('%s.lo5_out.fa' % fname),
165                       ph.outFile('%s.lo5.fa' % fname)),
166                      (ph.inFile('%s.lo5.stdout' % fname),
167                       ph.outFile('%s.lo5.stdout' % fname))])
171             redir_stdout=ph.outFile('%s.hi5.stdout' % fname),
173                   '-s', ph.inFile('%s.fa' % fname),
174                   '-o', ph.outFile('%s.hi5.fa' % fname)],
175             to_diff=[(ph.inFile('%s.hi5_out.fa' % fname),
176                       ph.outFile('%s.hi5.fa' % fname)),
177                      (ph.inFile('%s.hi5.stdout' % fname),
178                       ph.outFile('%s.hi5.stdout' % fname))])
182     for fname in ['1aab', '1ad2', '2trx']:
187                 redir_stdout=ph.outFile('%s.c%s.stdout' % (fname, c)),
189                       '-s', ph.inFile('%s.fa' % fname),
190                       '-o', ph.outFile('%s.c%s.fa' % (fname, c))],
191                 to_diff=[(ph.inFile('%s.c%s_out.fa' % (fname, c)),
192                           ph.outFile('%s.c%s.fa' % (fname, c))),
193                          (ph.inFile('%s.c%s.stdout' % (fname, c)),
194                           ph.outFile('%s.c%s.stdout' % (fname, c)))])