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src/b/i/biopython-1.63/Bio/AlignIO/NexusIO.py   biopython(Download)
    meaning this iterator will only yield one MultipleSeqAlignment.
    """
    n = Nexus.Nexus(handle)
    if not n.matrix:
        #No alignment found
                         + "format datatype=%s; end;"  \
                         % self._classify_alphabet_for_nexus(alignment._alphabet)
        n = Nexus.Nexus(minimal_record)
        n.alphabet = alignment._alphabet
        for record in alignment:

src/b/i/biopython-HEAD/Bio/AlignIO/NexusIO.py   biopython(Download)
    meaning this iterator will only yield one MultipleSeqAlignment.
    """
    n = Nexus.Nexus(handle)
    if not n.matrix:
        #No alignment found
                         + "format datatype=%s; end;"  \
                         % self._classify_alphabet_for_nexus(alignment._alphabet)
        n = Nexus.Nexus(minimal_record)
        n.alphabet = alignment._alphabet
        for record in alignment:

src/b/i/biopython-1.63/Bio/Phylo/NexusIO.py   biopython(Download)
    eventually change Nexus to use the new NewickIO parser directly.)
    """
    nex = Nexus.Nexus(handle)
 
    # NB: Once Nexus.Trees is modified to use Tree.Newick objects, do this:

src/b/i/biopython-HEAD/Bio/Phylo/NexusIO.py   biopython(Download)
    eventually change Nexus to use the new NewickIO parser directly.)
    """
    nex = Nexus.Nexus(handle)
 
    # NB: Once Nexus.Trees is modified to use Tree.Newick objects, do this:

src/c/g/cgat-HEAD/CGAT/TreeTools.py   cgat(Download)
 
import Bio
from Bio.Nexus.Nexus import Nexus
from Bio.Nexus.Trees import Tree
 
    # previoulsy, a string was ok, now a string
    # is interpreted as a filename.
    nexus = Nexus(StringIO.StringIO("".join(lines)))
 
    if len(nexus.trees) == 0:

src/c/g/CGAT-0.2.0/CGAT/TreeTools.py   CGAT(Download)
 
import Bio
from Bio.Nexus.Nexus import Nexus
from Bio.Nexus.Trees import Tree
 
    ## previoulsy, a string was ok, now a string
    ## is interpreted as a filename.
    nexus = Nexus( StringIO.StringIO("".join(lines)))
 
    if len(nexus.trees) == 0:

src/c/g/cgat-HEAD/scripts/tree_collapse_species.py   cgat(Download)
    lines = ["#NEXUS\nBegin trees;\ntree tree = "] + \
        sys.stdin.readlines() + ["End;"]
    nexus = Nexus.Nexus(string.join(lines, ""))
 
    if len(nexus.trees) != 1:

src/i/v/ivy-phylo-20120228/ivy/nexus.py   ivy-phylo(Download)
def fetchaln(fname):
    n = Nexus.Nexus(fname)
    return n
 
def split_blocks(infile):

src/b/i/biopython-HEAD/Tests/test_Nexus.py   biopython(Download)
        if os.path.isfile(filename):
            os.remove(filename)
        n = Nexus.Nexus(self.handle)
        n.write_nexus_data(filename)
        self.assertTrue(os.path.isfile(filename))
    def test_NexusTest1(self):
        """Test Nexus module"""
        # check data of main nexus file
        n=Nexus.Nexus(self.handle)
        self.assertEqual(os.path.normpath(n.filename),
                           exclude=n.invert(n.charsets['big']))
        f1.seek(0)
        nf1=Nexus.Nexus(f1)
        self.assertEqual(os.path.normpath(nf1.filename),
                         os.path.normpath(f1.name))
                           exclude=list(range(3, 40, 4)))
        f2.seek(0)
        nf2=Nexus.Nexus(f2)
        self.assertEqual(os.path.normpath(nf2.filename),
                         os.path.normpath(f2.name))
    def test_TreeTest1(self):
        """Test Tree module."""
        n=Nexus.Nexus(self.handle)
        t3=n.trees[2]
        t2=n.trees[2]

src/b/i/biopython-1.63/Tests/test_Nexus.py   biopython(Download)
        if os.path.isfile(filename):
            os.remove(filename)
        n = Nexus.Nexus(self.handle)
        n.write_nexus_data(filename)
        self.assertTrue(os.path.isfile(filename))
    def test_NexusTest1(self):
        """Test Nexus module"""
        # check data of main nexus file
        n=Nexus.Nexus(self.handle)
        self.assertEqual(os.path.normpath(n.filename),
                           exclude=n.invert(n.charsets['big']))
        f1.seek(0)
        nf1=Nexus.Nexus(f1)
        self.assertEqual(os.path.normpath(nf1.filename),
                         os.path.normpath(f1.name))
                           exclude=list(range(3, 40, 4)))
        f2.seek(0)
        nf2=Nexus.Nexus(f2)
        self.assertEqual(os.path.normpath(nf2.filename),
                         os.path.normpath(f2.name))
    def test_TreeTest1(self):
        """Test Tree module."""
        n=Nexus.Nexus(self.handle)
        t3=n.trees[2]
        t2=n.trees[2]