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src/c/o/cogent-1.5.3/tests/test_app/test_blast.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.parse.blast import QMEBlast9
from cogent.app.blast import seqs_to_stream,\
    make_subject_match_scorer, make_shotgun_scorer, keep_everything_scorer, \
    ids_from_seq_lower_threshold, PsiBlast, psiblast_n_neighbors
        #the command below should result in finding itself and 2554
        #it should run for max_iterations
        result = ids_from_seq_lower_threshold(query, n=12, \
                max_iterations=4, app=app, core_threshold=1e-50, \
                lower_threshold=1e-20, step=10000)
        #if n=2, it should find the same sequences but only run for 1 iteration
        #since it would hit n after the first blast search
        result = ids_from_seq_lower_threshold(query, n=2, \
                max_iterations=4, app=app, core_threshold=1e-50, \
                lower_threshold=1e-20, step=10000)
        #query_2_s e-value for itself is 9e-47, it should not be found
        #with the lower_threshold set to 1e-48
        result = ids_from_seq_lower_threshold(query, n=12, \
                max_iterations=4, app=app, core_threshold=1e-50, \
                lower_threshold=1e-48, step=10000)
        self.assertEqual(result[0], [])
        #it also should not be found if the max_iterations is set to 1
        result = ids_from_seq_lower_threshold(query, n=12, \

src/p/y/pycogent-HEAD/tests/test_app/test_blast.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.parse.blast import QMEBlast9
from cogent.app.blast import seqs_to_stream,\
    make_subject_match_scorer, make_shotgun_scorer, keep_everything_scorer, \
    ids_from_seq_lower_threshold, PsiBlast, psiblast_n_neighbors
        #the command below should result in finding itself and 2554
        #it should run for max_iterations
        result = ids_from_seq_lower_threshold(query, n=12, \
                max_iterations=4, app=app, core_threshold=1e-50, \
                lower_threshold=1e-20, step=10000)
        #if n=2, it should find the same sequences but only run for 1 iteration
        #since it would hit n after the first blast search
        result = ids_from_seq_lower_threshold(query, n=2, \
                max_iterations=4, app=app, core_threshold=1e-50, \
                lower_threshold=1e-20, step=10000)
        #query_2_s e-value for itself is 9e-47, it should not be found
        #with the lower_threshold set to 1e-48
        result = ids_from_seq_lower_threshold(query, n=12, \
                max_iterations=4, app=app, core_threshold=1e-50, \
                lower_threshold=1e-48, step=10000)
        self.assertEqual(result[0], [])
        #it also should not be found if the max_iterations is set to 1
        result = ids_from_seq_lower_threshold(query, n=12, \