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src/b/i/biopython-1.63/Doc/examples/www_blast.py   biopython(Download)
# option 2 -- create a handle from the string and parse it
string_result_handle = StringIO(blast_results)
b_record = NCBIXML.read(string_result_handle)
 
# now get the alignment info for all e values greater than some threshold

src/b/i/biopython-HEAD/Doc/examples/www_blast.py   biopython(Download)
# option 2 -- create a handle from the string and parse it
string_result_handle = StringIO(blast_results)
b_record = NCBIXML.read(string_result_handle)
 
# now get the alignment info for all e values greater than some threshold

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/g/i/giraffe-2.0/src/giraffe/features.py   giraffe(Download)
 
  with open(outfile, "r") as f:
    blast_record = NCBIXML.read(f)
    for alignment in blast_record.alignments:
      accession = Blast_Accession(alignment.accession)
 
  with open(outfile, "r") as f:
    blast_record = NCBIXML.read(f)
    for alignment in blast_record.alignments:
      for hsp in alignment.hsps:

src/b/c/bcbio-phyloblast-0.1.2/bcbio/phylo/blast.py   bcbio-phyloblast(Download)
            result = result.replace(problem, " ")
        try:
            rec = NCBIXML.read(StringIO.StringIO(result))
        except (xml.parsers.expat.ExpatError, ValueError):
            rec = None

src/b/i/biopython-1.63/Tests/test_NCBIXML.py   biopython(Download)
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 

src/b/i/biopython-HEAD/Tests/test_NCBIXML.py   biopython(Download)
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 
 
        handle = open(datafile)
        record = NCBIXML.read(handle)
        handle.close()
 

src/b/i/biopython-HEAD/Tests/test_NCBI_qblast.py   biopython(Download)
        #e.g. a proxy error
        raise MissingExternalDependencyError("internet connection failed")
    record = NCBIXML.read(handle)
 
    if record.query == "No definition line":

src/b/i/biopython-1.63/Tests/test_NCBI_qblast.py   biopython(Download)
        #e.g. a proxy error
        raise MissingExternalDependencyError("internet connection failed")
    record = NCBIXML.read(handle)
 
    if record.query == "No definition line":