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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
    if refseqs_fp:
        blast_db, db_files_to_remove =\
         build_blast_db_from_fasta_path(refseqs_fp,
                                        output_dir=WorkingDir,
                                        is_protein=is_protein)

src/q/i/qiime-1.8.0/qiime/pick_otus.py   qiime(Download)
from cogent.app.cd_hit import cdhit_clusters_from_seqs
from cogent.app.mothur import Mothur
from cogent.app.formatdb import build_blast_db_from_fasta_path
from cogent.app.blast import blast_seqs, Blastall, BlastResult
from cogent.core.sequence import DnaSequence
        if not blast_db:
            self.blast_db, self.db_files_to_remove = \
                build_blast_db_from_fasta_path(abspath(refseqs_fp),
                 is_protein=self.Params['is_protein'],
                 output_dir=get_qiime_temp_dir())

src/q/i/qiime-1.8.0/qiime/parallel/identify_chimeric_seqs.py   qiime(Download)
from os.path import split
from shutil import copy
from cogent.app.formatdb import build_blast_db_from_fasta_path
from cogent.parse.fasta import MinimalFastaParser
from qiime.identify_chimeric_seqs import make_cidx_file
    def _precommand_initiation(self, input_fp, output_dir, working_dir,
                               params):
        if params['chimera_detection_method'] == 'blast_fragments':
            blast_db, db_files_to_remove = \
                 build_blast_db_from_fasta_path(params['reference_seqs_fp'],
            #and parallel jobs clash
            _, db_files_to_remove = \
                 build_blast_db_from_fasta_path(reference_seqs_fp)
            self.files_to_remove += db_files_to_remove
 

src/q/i/qiime-1.8.0/qiime/parallel/align_seqs.py   qiime(Download)
__email__ = "gregcaporaso@gmail.com"
 
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.align_seqs import compute_min_alignment_length
from qiime.parallel.util import ParallelWrapper
            # will then access one db rather than create one per proc
            blast_db, db_files_to_remove = \
             build_blast_db_from_fasta_path(params['template_fp'],
                                            output_dir=get_qiime_temp_dir())
            self.files_to_remove += db_files_to_remove

src/q/i/qiime-1.8.0/qiime/parallel/blast.py   qiime(Download)
 
from os.path import split, splitext
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.util import load_qiime_config, get_options_lookup
 
            # will then access one db rather than create one per proc.
            blast_db, db_files_to_remove = \
                 build_blast_db_from_fasta_path(params['refseqs_path'])
            self.files_to_remove += db_files_to_remove
            params['blast_db'] = blast_db

src/q/i/qiime-1.8.0/qiime/parallel/pick_otus.py   qiime(Download)
__email__ = "gregcaporaso@gmail.com"
 
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.parallel.util import ParallelWrapper, BufferedWriter
from qiime.parallel.poller import basic_process_run_results_f
            # will then access one db rather than create one per proc
            blast_db, db_files_to_remove = \
                 build_blast_db_from_fasta_path(params['refseqs_fp'])
            self.files_to_remove += db_files_to_remove
            params['blast_db'] = blast_db

src/q/i/qiime-1.8.0/qiime/parallel/assign_taxonomy.py   qiime(Download)
__email__ = "jai.rideout@gmail.com"
 
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.parallel.util import ParallelWrapper
 
            # will then access one db rather than create one per proc.
            blast_db, db_files_to_remove = \
                 build_blast_db_from_fasta_path(params['reference_seqs_fp'])
            self.files_to_remove += db_files_to_remove
            params['blast_db'] = blast_db

src/q/i/qiime-1.8.0/qiime/identify_chimeric_seqs.py   qiime(Download)
from cogent.util.misc import remove_files, app_path
from cogent.parse.fasta import MinimalFastaParser
from cogent.app.formatdb import build_blast_db_from_fasta_path
from cogent.app.parameters import ValuedParameter, FlagParameter
from cogent.app.util import CommandLineApplication, ResultPath,\
                 "refseqs_fp or blast_db must be provided to  %s" % self.Name
            blast_db, self._db_files_to_remove = \
             build_blast_db_from_fasta_path(reference_seqs_fp)
        else:
            blast_db = params['blast_db']

src/q/i/qiime-1.8.0/qiime/assign_taxonomy.py   qiime(Download)
 
from cogent import LoadSeqs, DNA
from cogent.app.formatdb import build_blast_db_from_fasta_path
from cogent.app.blast import blast_seqs, Blastall, BlastResult
from cogent.app import rtax
            refseqs_dir, refseqs_name = os.path.split(reference_seqs_path)
            blast_db, db_files_to_remove = \
             build_blast_db_from_fasta_path(reference_seqs_path)
 
        # build the mapping of sequence identifier

src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
from cogent.align.align import make_dna_scoring_dict, global_pairwise
from cogent.app.blast import blastn
from cogent.app.formatdb import build_blast_db_from_seqs, \
 build_blast_db_from_fasta_path
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs

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