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src/p/y/pytools-HEAD/blast.py   pytools(Download)
def number_genome_qblast_hits(seqreclist):
    fastastring = ''.join([rec.format('fasta') for rec in seqreclist])
    results_handle = NCBIWWW.qblast('blastn','nr',fastastring,expect=1.,word_size=7,nucl_reward=1,nucl_penalty=-3,hitlist_size=1000)
    blast_records = NCBIXML.parse(results_handle)
 
def number_genome_qblast_protein_hits(sequence):
    results_handle = NCBIWWW.qblast('blastp','nr',sequence,expect=100,word_size=3,hitlist_size=1000)
    blast_records = NCBIXML.parse(results_handle)
    num_hits = sum([len(record.alignments) for record in blast_records])
    return num_hits

src/b/i/biopython-1.63/Doc/examples/www_blast.py   biopython(Download)
 
print('Doing the BLAST and retrieving the results...')
result_handle = NCBIWWW.qblast('blastn', 'nr', f_record.format('fasta'))
 
# save the results for later, in case we want to look at it

src/b/i/biopython-HEAD/Doc/examples/www_blast.py   biopython(Download)
 
print('Doing the BLAST and retrieving the results...')
result_handle = NCBIWWW.qblast('blastn', 'nr', f_record.format('fasta'))
 
# save the results for later, in case we want to look at it

src/b/i/biskit-2.4/Biskit/Mod/SequenceSearcher.py   biskit(Download)
                self.log.add('starting blast query...')
 
            results = NCBIWWW.qblast( program=method, database=db,
                                      sequence=query, expect=e,
                                      ncbi_gi='FALSE', **kw )

src/i/v/ivy-phylo-20120228/ivy/genbank.py   ivy-phylo(Download)
def blast_closest(fasta, e=10):
    f = NCBIWWW.qblast("blastn", "nr", fasta, expect=e, hitlist_size=1)
    rec = NCBIXML.read(f)
    d = rec.descriptions[0]
    result = Storage()
def blast(query, e=10, n=100, entrez_query=""):
    f = NCBIWWW.qblast("blastn", "nr", query, expect=e, hitlist_size=n,
                       entrez_query=entrez_query)
    rec = NCBIXML.read(f)
    v = []

src/b/i/biopython-1.63/Tests/test_NCBI_qblast.py   biopython(Download)
        if program=="blastn":
            #Check the megablast parameter is accepted
            handle = NCBIWWW.qblast(program, database, query,
                                    alignments=10, descriptions=10,
                                    hitlist_size=10,
                                    entrez_query=entrez_filter,
                                    expect=e_value, megablast="FALSE")
        else:
            handle = NCBIWWW.qblast(program, database, query,

src/b/i/biopython-HEAD/Tests/test_NCBI_qblast.py   biopython(Download)
        if program=="blastn":
            #Check the megablast parameter is accepted
            handle = NCBIWWW.qblast(program, database, query,
                                    alignments=10, descriptions=10,
                                    hitlist_size=10,
                                    entrez_query=entrez_filter,
                                    expect=e_value, megablast="FALSE")
        else:
            handle = NCBIWWW.qblast(program, database, query,

src/o/l/oligotyping-HEAD/Oligotyping/utils/blast.py   oligotyping(Download)
    def search(self, sequence, output_file = None):
        result_handle = NCBIWWW.qblast("blastn", "nt", sequence.replace('-', ''))
        result = result_handle.read()
 
        if output_file:

src/b/c/bcbb-HEAD/visualize/blast_conservation_plot.py   bcbb(Download)
            search_gi))
        if not os.path.exists(out_file):
            blast_handle = NCBIWWW.qblast(blast_method, "nr", search_gi)
            with open(out_file, 'w') as out_handle:
                for line in blast_handle: