Bio.Blast.Applications.NcbitblastnCommandline

All Samples(4) | Call(3) | Derive(0) | Import(1)

Wrapper for the NCBI BLAST+ program tblastn.

With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI
replaced the old blastall tool with separate tools for each of the searches.
This wrapper therefore replaces BlastallCommandline with option -p tblastn.

>>> from Bio.Blast.Applications import NcbitblastnCommandline
>>> cline = NcbitblastnCommandline(help=True)
>>> cline
NcbitblastnCommandline(cmd='tblastn', help=True)(more...)

src/s/e/SeqFindR-0.31/SeqFindR/blast.py SeqFindR(Download)

from Bio.Blast              import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbitblastnCommandline
from Bio.Blast.Applications import NcbitblastxCommandline

    if protein:
        sys.stderr.write('Using tblastn\n')
        run_command = NcbitblastnCommandline(query=query, seg='no',
                    db=database, outfmt=5, num_threads=args.BLAST_THREADS,
                    max_target_seqs=1, evalue=args.evalue, out='blast.xml')

src/b/i/biopython-1.63/Tests/test_NCBI_BLAST_tools.py biopython(Download)

    def test_tblastn(self):
        """Pairwise TBLASTN search"""
        global exe_names
        cline = Applications.NcbitblastnCommandline(exe_names["tblastn"],
                        query="GenBank/NC_005816.faa",

src/b/i/biopython-HEAD/Tests/test_NCBI_BLAST_tools.py biopython(Download)

    def test_tblastn(self):
        """Pairwise TBLASTN search"""
        global exe_names
        cline = Applications.NcbitblastnCommandline(exe_names["tblastn"],
                        query="GenBank/NC_005816.faa",