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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
        output.cleanUp()
        if result:
            ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
        num_ids = len(ids)
        if num_ids >= n:
        result = list(output.get('BlastOut', output['StdOut']))
        if result:
            ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
        num_ids = len(ids)
        if num_ids >= n:
                result = list(output.get('BlastOut', output['StdOut']))
 
            ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
            output.cleanUp()
            all_ids[i + 1] = (core_threshold, copy(ids))

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
        output.cleanUp()
        if result:
            ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
        num_ids = len(ids)
        if num_ids >= n:
        result = list(output.get('BlastOut', output['StdOut']))
        if result:
            ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
        num_ids = len(ids)
        if num_ids >= n:
                result = list(output.get('BlastOut', output['StdOut']))
 
            ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
            output.cleanUp()
            all_ids[i + 1] = (core_threshold, copy(ids))

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, \
    def test_LastProteinIds9(self):
        """LastProteinIds9 should give last protein ids in iter"""
        result = LastProteinIds9(self.rec)
        self.assertEqual(result, ['ece:Z4181', 'ecs:ECs3717', 'cvi:CV2421',\
            'sfl:CP0138', 'spt:SPA2730', 'sec:SC2804', 'stm:STM2872'])
        #should also work if threshold set
        result = LastProteinIds9(self.rec, False, threshold=8e-6)

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, \
    def test_LastProteinIds9(self):
        """LastProteinIds9 should give last protein ids in iter"""
        result = LastProteinIds9(self.rec)
        self.assertEqual(result, ['ece:Z4181', 'ecs:ECs3717', 'cvi:CV2421',\
            'sfl:CP0138', 'spt:SPA2730', 'sec:SC2804', 'stm:STM2872'])
        #should also work if threshold set
        result = LastProteinIds9(self.rec, False, threshold=8e-6)