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src/b/c/bcbio-phyloblast-0.1.2/bcbio/phylo/blast.py   bcbio-phyloblast(Download)
import StringIO
 
from Bio.Blast.Applications import NcbiblastpCommandline
from Bio.Blast import NCBIXML
from Bio import SeqIO
def _compare_by_blast_hitlist(query, xref_db, blast_out, thresh):
    cl = NcbiblastpCommandline(query=query, db=xref_db, out=blast_out,
            outfmt=6, num_descriptions=10000, num_alignments=0, evalue=thresh)
    subprocess.check_call(str(cl).split())
    hits = []
def _compare_by_blast_2seq(query, subject, blast_out):
    """Compare two sequences by BLAST without output database.
    """
    cl = NcbiblastpCommandline(query=query, subject=subject, out=blast_out,
            outfmt=6, num_descriptions=1, num_alignments=1)
    if blast_cmd is None:
        blast_cmd = "blastp"
    cl = NcbiblastpCommandline(cmd=blast_cmd, query=input_ref, db=xref_db,
                               out=blast_out, outfmt=5, num_descriptions=1,
                               num_alignments=1)

src/d/u/DuctApe-0.16.4/ductape/genome/blast.py   DuctApe(Download)
    def runBlast(self, queryFile, db, outFile='', evalue = 10,
                    task = '', ncpus = 1, additional = '', outfmt='5'):
        '''Run Blast with the desired parameters'''
        # Create the command line
        from Bio.Blast.Applications import NcbiblastpCommandline
        self._out = outFile
        cmd = NcbiblastpCommandline(db=db,

src/b/i/biopython-1.63/Tests/test_NCBI_BLAST_tools.py   biopython(Download)
    def test_blastp(self):
        """Pairwise BLASTP search"""
        global exe_names
        cline = Applications.NcbiblastpCommandline(exe_names["blastp"],
                        query="Fasta/rose.pro",

src/b/i/biopython-HEAD/Tests/test_NCBI_BLAST_tools.py   biopython(Download)
    def test_blastp(self):
        """Pairwise BLASTP search"""
        global exe_names
        cline = Applications.NcbiblastpCommandline(exe_names["blastp"],
                        query="Fasta/rose.pro",