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python-biopython  1.60
Classes | Functions | Variables
test_EmbossPhylipNew Namespace Reference

Classes

class  DistanceTests
class  ParsimonyTests
class  BootstrapTests
class  TreeComparisonTests

Functions

def write_AlignIO_dna
def write_AlignIO_protein
def clean_up
def parse_trees

Variables

list exes_wanted
tuple exes = dict()
list path = os.environ["EMBOSS_ROOT"]
tuple output = commands.getoutput("%s -help" % name)
tuple runner = unittest.TextTestRunner(verbosity = 2)

Function Documentation

Delete tests files (to be used as tearDown() function in test fixtures)

Definition at line 64 of file test_EmbossPhylipNew.py.

00064 
00065 def clean_up():
00066     """Delete tests files (to be used as tearDown() function in test fixtures)"""
00067     for filename in ["test_file", "Phylip/opuntia.phy","Phylip/hedgehog.phy"]:
00068         if os.path.isfile(filename):
00069             os.remove(filename)

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Helper function until we have Bio.Phylo on trunk.

Definition at line 70 of file test_EmbossPhylipNew.py.

00070 
00071 def parse_trees(filename):
00072     """Helper function until we have Bio.Phylo on trunk."""
00073     data = open("test_file", "r").read()
00074     for tree_str in data.split(";\n"):
00075         if tree_str:
00076             yield Trees.Tree(tree_str+";")

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Convert opuntia.aln to a phylip file

Definition at line 54 of file test_EmbossPhylipNew.py.

00054 
00055 def write_AlignIO_dna():
00056     """Convert opuntia.aln to a phylip file"""
00057     assert 1 == AlignIO.convert("Clustalw/opuntia.aln", "clustal",
00058                                 "Phylip/opuntia.phy", "phylip")

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Convert hedgehog.aln to a phylip file

Definition at line 59 of file test_EmbossPhylipNew.py.

00059 
00060 def write_AlignIO_protein():
00061     """Convert hedgehog.aln to a phylip file"""
00062     assert 1 == AlignIO.convert("Clustalw/hedgehog.aln", "clustal",
00063                                 "Phylip/hedgehog.phy", "phylip")

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Variable Documentation

tuple test_EmbossPhylipNew.exes = dict()

Definition at line 25 of file test_EmbossPhylipNew.py.

Initial value:
00001 ['fdnadist', 'fneighbor', 'fprotdist','fprotpars','fconsense',
00002                'fseqboot', 'ftreedist', 'fdnapars']

Definition at line 23 of file test_EmbossPhylipNew.py.

tuple test_EmbossPhylipNew.output = commands.getoutput("%s -help" % name)

Definition at line 40 of file test_EmbossPhylipNew.py.

list test_EmbossPhylipNew.path = os.environ["EMBOSS_ROOT"]

Definition at line 30 of file test_EmbossPhylipNew.py.

tuple test_EmbossPhylipNew.runner = unittest.TextTestRunner(verbosity = 2)

Definition at line 287 of file test_EmbossPhylipNew.py.