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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",