Exemplos de SuperTreeSupport em Python

Exemplo n.º 1

Arquivo: sDoSTS.py Projeto: sdwfrost/p4-phylogeny

read('inTrees.phy')
inTrees = var.trees
var.trees = []
read('stMcmcCons.nex')
read('mrpMajRuleConsTree.nex')
read('mrpStrictConsTree.nex')
var.trees[1].name = 'mrpMajRule'
var.trees[2].name = 'mrpStrict'

from p4.SuperTreeSupport import SuperTreeSupport
print("%20s  %6s  %6s  %6s  %6s  %6s" % (' ', 'S', 'P', 'Q', 'R', 'V'))
for st in var.trees:

    sts = SuperTreeSupport(st, inTrees)

    sts.doSaveDecoratedTree = False
    sts.decoratedFilename = 'mytree.nex'
    sts.doSaveIndexTree = False
    sts.indexFilename = 'mytreeIndex.nex'
    sts.csvFilename = 'mytreeIndex.csv'
    sts.doDrawTree = False
    sts.verbose = 0

    sts.superTreeSupport()
    print("%20s  %6.2f  %6.2f  %6.2f  %6.2f  %6.2f" %
          (st.name, sts.S, sts.P, sts.Q, sts.R, sts.V))

Exemplo n.º 2

Arquivo: sDoSTS.py Projeto: pgfoster/p4-phylogenetics

read('inTrees.phy')
inTrees = var.trees
var.trees = []
read('stMcmcCons.nex')
read('mrpMajRuleConsTree.nex')
read('mrpStrictConsTree.nex')
var.trees[1].name = 'mrpMajRule'
var.trees[2].name = 'mrpStrict'


from p4.SuperTreeSupport import SuperTreeSupport
print "%20s  %6s  %6s  %6s  %6s  %6s" % (' ', 'S', 'P', 'Q', 'R', 'V')
for st in var.trees:
    
    sts = SuperTreeSupport(st, inTrees)
    
    sts.doSaveDecoratedTree = False
    sts.decoratedFilename='mytree.nex'
    sts.doSaveIndexTree=False
    sts.indexFilename='mytreeIndex.nex'
    sts.csvFilename='mytreeIndex.csv'
    sts.doDrawTree=False
    sts.verbose=0
    
    sts.superTreeSupport()
    print "%20s  %6.2f  %6.2f  %6.2f  %6.2f  %6.2f" % (st.name, sts.S, sts.P, sts.Q, sts.R, sts.V)
    

Exemplo n.º 3

Arquivo: sSuperTreeSupport.py Projeto: Anaphory/p4-phylogeny

from p4.SuperTreeSupport import SuperTreeSupport

sts = SuperTreeSupport('supertree.nex', 'input.nex')
sts.doSaveDecoratedTree = False
sts.decoratedFilename='mytree.nex'
sts.verbose=2
sts.doDrawTree=True
sts.superTreeSupport()

Exemplo n.º 4

Arquivo: sSuperTreeSupport.py Projeto: sdwfrost/p4-phylogeny

from p4.SuperTreeSupport import SuperTreeSupport

sts = SuperTreeSupport('supertree.nex', 'input.nex')
sts.doSaveDecoratedTree = False
sts.decoratedFilename = 'mytree.nex'
sts.verbose = 2
sts.doDrawTree = True
sts.superTreeSupport()