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src/c/o/cogent-1.5.3/cogent/app/blast.py   cogent(Download)
    get_tmp_filename, guess_input_handler, ApplicationNotFoundError
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
from random import choice

src/p/y/pycogent-HEAD/cogent/app/blast.py   pycogent(Download)
    get_tmp_filename, guess_input_handler, ApplicationNotFoundError
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
from random import choice

src/c/o/cogent-1.5.3/tests/test_parse/test_blast.py   cogent(Download)
from string import split, strip
from cogent.util.unit_test import TestCase, main
from cogent.parse.blast import iter_finder, query_finder, iteration_set_finder,\
    is_blast_junk, is_blat_junk, make_label, PsiBlastQueryFinder, \
    TableToValues, \

src/p/y/pycogent-HEAD/tests/test_parse/test_blast.py   pycogent(Download)
from string import split, strip
from cogent.util.unit_test import TestCase, main
from cogent.parse.blast import iter_finder, query_finder, iteration_set_finder,\
    is_blast_junk, is_blat_junk, make_label, PsiBlastQueryFinder, \
    TableToValues, \

src/c/o/cogent-1.5.3/tests/test_app/test_blast.py   cogent(Download)
from glob import glob
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, \
        qm3 = make_subject_match_scorer(3)
        qm5 = make_subject_match_scorer(5)
        qmes = wrap_qmes(QMEBlast9(self.rec3))
        self.assertEqualItems(qm1(qmes), ['ece:Z4181','ece:Z4182','ece:Z4183'])
        self.assertEqualItems(qm3(qmes), ['ece:Z4181','ece:Z4183'])
        sg4 = make_shotgun_scorer(4)
        sg5 = make_shotgun_scorer(5)
        qmes = wrap_qmes(QMEBlast9(self.rec3))
        self.assertEqualItems(sg1(qmes), keep_everything_scorer(qmes))
        self.assertEqualItems(sg2(qmes), \
    def test_keep_everything_scorer(self):
        """keep_everything_scorer should keep all ids found."""
        k = keep_everything_scorer(wrap_qmes(QMEBlast9(self.rec2)))
        self.assertEqualItems(k, \
            ['ece:Z4181','ecs:ECs3717','spt:SPA2730','cvi:CV2421','ece:Z4182'])

src/p/y/pycogent-HEAD/tests/test_app/test_blast.py   pycogent(Download)
from glob import glob
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, \
        qm3 = make_subject_match_scorer(3)
        qm5 = make_subject_match_scorer(5)
        qmes = wrap_qmes(QMEBlast9(self.rec3))
        self.assertEqualItems(qm1(qmes), ['ece:Z4181','ece:Z4182','ece:Z4183'])
        self.assertEqualItems(qm3(qmes), ['ece:Z4181','ece:Z4183'])
        sg4 = make_shotgun_scorer(4)
        sg5 = make_shotgun_scorer(5)
        qmes = wrap_qmes(QMEBlast9(self.rec3))
        self.assertEqualItems(sg1(qmes), keep_everything_scorer(qmes))
        self.assertEqualItems(sg2(qmes), \
    def test_keep_everything_scorer(self):
        """keep_everything_scorer should keep all ids found."""
        k = keep_everything_scorer(wrap_qmes(QMEBlast9(self.rec2)))
        self.assertEqualItems(k, \
            ['ece:Z4181','ecs:ECs3717','spt:SPA2730','cvi:CV2421','ece:Z4182'])