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src/q/i/qiime-1.8.0/scripts/exclude_seqs_by_blast.py   qiime(Download)
from os import system, getcwd, makedirs
from os.path import join, split, abspath
from cogent.app.formatdb import FormatDb
from cogent.app.parameters import FilePath
from cogent.util.misc import remove_files
        subject_dir, subj_file = split(inpath)
 
        fdb = FormatDb(WorkingDir = subject_dir ) 
        # Currently we do not support protein blasts, but
        # this would be easy to add in the future...
            print "Formatting db with command: %s" %formatdb_cmd
 
        app_result = fdb(subject_db)
        formatdb_filepaths = []
        for v in app_result.values():

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_call(self):
        """FormatDb: Calling on a nucleotide data functions as expected
        """
        fdb = FormatDb(WorkingDir='/tmp')
        result = fdb(self.in_seqs1_fp)
    def test_blast_against_new_db(self):
        """Formatdb: blastall against a newly created DB functions as expected
        """
        fdb = FormatDb(WorkingDir='/tmp')
        result = fdb(self.in_seqs1_fp)

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_call(self):
        """FormatDb: Calling on a nucleotide data functions as expected
        """
        fdb = FormatDb(WorkingDir='/tmp')
        result = fdb(self.in_seqs1_fp)
    def test_blast_against_new_db(self):
        """Formatdb: blastall against a newly created DB functions as expected
        """
        fdb = FormatDb(WorkingDir='/tmp')
        result = fdb(self.in_seqs1_fp)