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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
        params = {'-j':11}
        lines = bdb_seqs.split('\n')
        results = psiblast_n_neighbors(lines, n=12, blast_db='test_bdb', \
                method='lower_threshold', params=params,\
                core_threshold=1e-50, step=10000)

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
        params = {'-j':11}
        lines = bdb_seqs.split('\n')
        results = psiblast_n_neighbors(lines, n=12, blast_db='test_bdb', \
                method='lower_threshold', params=params,\
                core_threshold=1e-50, step=10000)