Python krona Examples

Example #1

File: test_metagenomics.py Project: tianyabeef/viral-ngs

 def test_krona_import_taxonomy(self):
     out_html = util.file.mkstempfname('.html')
     metagenomics.krona(self.inTsv, self.db, out_html, queryColumn=3, taxidColumn=5, scoreColumn=7,
                        noHits=True, noRank=True)
     self.mock_krona().import_taxonomy.assert_called_once_with(
         self.db, [self.inTsv], out_html, query_column=3, taxid_column=5, score_column=7,
         no_hits=True, no_rank=True)

Example #2

File: test_metagenomics.py Project: sudarshangc/viral-ngs

 def test_krona_import_taxonomy(self):
     out_html = util.file.mkstempfname('.html')
     metagenomics.krona(self.inTsv, self.db, out_html, queryColumn=3, taxidColumn=5, scoreColumn=7,
                        noHits=True, noRank=True, inputType='tsv')
     self.mock_krona().import_taxonomy.assert_called_once_with(
         self.db, [self.inTsv], out_html, query_column=3, taxid_column=5, score_column=7,
         no_hits=True, no_rank=True, magnitude_column=None, root_name=os.path.basename(self.inTsv))

Example #3

File: test_metagenomics.py Project: broadinstitute/viral-ngs

 def test_krona_import_taxonomy(self):
     out_html = util.file.mkstempfname('.html')
     metagenomics.krona(self.inTsv, self.db, out_html, queryColumn=3, taxidColumn=5, scoreColumn=7,
                        noHits=True, noRank=True, inputType='tsv')
     self.mock_krona().import_taxonomy.assert_called_once_with(
         self.db, [self.inTsv], out_html, query_column=3, taxid_column=5, score_column=7,
         no_hits=True, no_rank=True, magnitude_column=None, root_name=os.path.basename(self.inTsv))

Example #4

 def test_krona_import_taxonomy(self):
     out_html = util.file.mkstempfname('.html')
     metagenomics.krona(self.inTsv,
                        self.db,
                        out_html,
                        queryColumn=3,
                        taxidColumn=5,
                        scoreColumn=7,
                        noHits=True,
                        noRank=True)
     self.mock_krona().import_taxonomy.assert_called_once_with(
         self.db, [self.inTsv],
         out_html,
         query_column=3,
         taxid_column=5,
         score_column=7,
         no_hits=True,
         no_rank=True)