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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",