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src/q/i/qiime-1.8.0/qiime/util.py   qiime(Download)
from cogent.util.misc import remove_files
from cogent.util.dict2d import Dict2D
from cogent.app.formatdb import build_blast_db_from_fasta_path,\
    build_blast_db_from_fasta_file
from cogent import LoadSeqs
    elif refseqs:
        blast_db, db_files_to_remove =\
         build_blast_db_from_fasta_file(refseqs,
                                        output_dir=WorkingDir,
                                        is_protein=is_protein)

src/c/o/cogent-1.5.3/tests/test_app/test_formatdb.py   cogent(Download)
from cogent.util.misc import remove_files
from cogent.app.blast import blastn
from cogent.app.formatdb import FormatDb, build_blast_db_from_seqs,\
    build_blast_db_from_fasta_path, build_blast_db_from_fasta_file
 
    def test_build_blast_db_from_fasta_file(self):
        """build_blast_db_from_fasta_file works with open files as input
        """
        blast_db, db_files = \
         build_blast_db_from_fasta_file(open(self.in_aln1_fp),output_dir='/tmp/')

src/p/y/pycogent-HEAD/tests/test_app/test_formatdb.py   pycogent(Download)
from cogent.util.misc import remove_files
from cogent.app.blast import blastn
from cogent.app.formatdb import FormatDb, build_blast_db_from_seqs,\
    build_blast_db_from_fasta_path, build_blast_db_from_fasta_file
 
    def test_build_blast_db_from_fasta_file(self):
        """build_blast_db_from_fasta_file works with open files as input
        """
        blast_db, db_files = \
         build_blast_db_from_fasta_file(open(self.in_aln1_fp),output_dir='/tmp/')

src/q/i/qiime-1.8.0/tests/test_util.py   qiime(Download)
from cogent.util.misc import remove_files
from cogent.cluster.procrustes import procrustes
from cogent.app.formatdb import build_blast_db_from_fasta_file
from cogent.util.misc import get_random_directory_name, remove_files
 
        self.inseqs1 = inseqs1.split('\n')
        self.blast_db, db_files_to_remove =\
          build_blast_db_from_fasta_file(self.refseqs1,
                                         output_dir=get_qiime_temp_dir())
        self.files_to_remove = db_files_to_remove

src/q/i/qiime-1.8.0/tests/test_identify_chimeric_seqs.py   qiime(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import remove_files
from cogent.app.formatdb import build_blast_db_from_fasta_file
 
from qiime.util import get_tmp_filename, create_dir
    def test_function_w_preexisting_blastdb(self):
        blast_db, db_files_to_remove = \
         build_blast_db_from_fasta_file(test_refseq_coll.toFasta().split('\n'))
        self._paths_to_clean_up += db_files_to_remove
        params = {'id_to_taxonomy_fp':self.id_to_taxonomy_fp,\