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Wrapper for the NCBI BLAST+ program blastn (for nucleotides).

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 blastn.

For example, to run a search against the "nt" nucleotide database using the
FASTA nucleotide file "m_code.fasta" as the query, with an expectation value
cut off of 0.001, saving the output to a file in XML format:
(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
            sys.stderr.write('Using blastn\n')
            if args.short == False:
                run_command = NcbiblastnCommandline(query=query, dust='no',
                            db=database, outfmt=5, 
                            num_threads=args.BLAST_THREADS,
                            max_target_seqs=1, evalue=args.evalue, 
                            out='blast.xml')
            else:
                sys.stderr.write('Optimising for short query sequences\n')
                run_command = NcbiblastnCommandline(query=query, dust='no',
 
    sys.stderr.write(str(run_command)+"\n")
    run_command()
    return os.path.join(os.getcwd(), 'blast.xml')
 

src/g/i/giraffe-2.0/src/giraffe/features.py   giraffe(Download)
 
 
from Bio.Blast.Applications import NcbiblastnCommandline, NcbiblastxCommandline
from Bio.Blast import NCBIXML
import tempfile
                                     evalue=evalue_threshold, word_size=3, outfmt=5, out=outfile)
  else:
    blast_cl = NcbiblastnCommandline(query=infile, db="%s" % (dbobj.dna_db_name(),),
                                     evalue=evalue_threshold, word_size=6, outfmt=5, out=outfile)
 
 
  outfile = "%s.out.xml" % (query_file,)
  blast_cl = NcbiblastnCommandline(query=query_file, subject=subject_file,
                                   evalue=0.001, word_size=6,
                                   # these params were tested to allow gaps in

src/p/i/picobio-HEAD/assembly_comparison/multi_comparison.py   picobio(Download)
from Bio.SeqIO.FastaIO import SimpleFastaParser
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Blast.Applications import NcbiblastnCommandline
 
from reportlab.lib import colors
    assert os.path.isfile(db_fasta + ".nin"), "Missing database for %s" % db_fasta
    assert os.path.isfile(db_fasta + ".nsq"), "Missing database for %s" % db_fasta
    cmd = NcbiblastnCommandline(query=query_fasta, db=db_fasta,
                                out=blast_file, outfmt=6,
                                evalue=1e-5)
    print cmd
    stdout, stderr = cmd()

src/p/i/picobio-HEAD/assembly_comparison/assembly_comparison.py   picobio(Download)
from Bio import SeqIO
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Blast.Applications import NcbiblastnCommandline
 
from reportlab.lib import colors
    assert os.path.isfile(db_fasta + ".nin")
    assert os.path.isfile(db_fasta + ".nsq")
    cmd = NcbiblastnCommandline(query=query_fasta, db=db_fasta,
                                out=blast_file, outfmt=6,
                                evalue=1e-5)
    print cmd
    stdout, stderr = cmd()

src/b/i/biopython-1.63/Tests/test_NCBI_BLAST_tools.py   biopython(Download)
    def test_blastn(self):
        """Pairwise BLASTN search"""
        global exe_names
        cline = Applications.NcbiblastnCommandline(exe_names["blastn"],
                        query="GenBank/NC_005816.ffn",

src/b/i/biopython-HEAD/Tests/test_NCBI_BLAST_tools.py   biopython(Download)
    def test_blastn(self):
        """Pairwise BLASTN search"""
        global exe_names
        cline = Applications.NcbiblastnCommandline(exe_names["blastn"],
                        query="GenBank/NC_005816.ffn",