本文整理汇总了Python中rasmus.util.mget函数的典型用法代码示例。如果您正苦于以下问题:Python mget函数的具体用法?Python mget怎么用?Python mget使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了mget函数的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: chi_square_fit
def chi_square_fit(cdf, params, data, ndivs=20, minsamples=5, plot=False,
start=-util.INF, end=util.INF):
from rasmus import gnuplot
import scipy
import scipy.stats
# determine ndiv and binsize
binsize = len(data) / ndivs
if binsize < minsamples:
ndivs = len(data) / minsamples
binsize = len(data) / ndivs
data = sorted(data)
bins = [data[i:i+binsize] for i in xrange(0, len(data), binsize)]
obs = scipy.array(map(len, bins))
ind = util.find(lambda x: x[-1] >= start and x[0] <= end, bins)
obs = util.mget(obs, ind)
x = [bin[0] for bin in bins]
expected = [len(data) * cdf(x[1], params)]
expected.extend([len(data) *
(cdf(x[i+1], params) - cdf(x[i], params))
for i in range(1, len(x)-1)])
expected.append(len(data) * (1.0 - cdf(x[-1], params)))
expected = scipy.array(util.mget(expected, ind))
chi2, pval = scipy.stats.chisquare(obs, expected)
if plot:
p = gnuplot.plot(util.mget(x, ind), obs)
p.plot(util.mget(x, ind), expected)
return chi2, pval
开发者ID:jeffhsu3,项目名称:argweaver,代码行数:34,代码来源:stats.py
示例2: _write_directive
def _write_directive(self, line, out, delim):
"""Write a directive"""
if line == DIR_VERSION:
out.write("##version:%s\n" % self.version)
elif line == DIR_TYPES:
if len(self) > 0:
entry = self[0]
else:
entry = [""] * len(self.headers)
out.write("##types:" +
self._type_lookup.formatTableTypes(
util.mget(self.types, self.headers),
delim) + "\n")
elif line == DIR_DEFAULTS:
out.write("##defaults:" +
delim.join(map(str,
util.mget(self.defaults, self.headers))) + "\n")
elif line == DIR_HEADERS:
out.write("##headers:%d\n" % self.nheaders)
else:
raise "unknown directive:", line
开发者ID:sarab609,项目名称:scraps,代码行数:25,代码来源:tablelib.py
示例3: init_distmats
def init_distmats(self):
"""Initialize distance matrices
Initialization should by done after trees and alignments
"""
if len(self.distmats) > 0:
self.matrices = []
# setup matrices
for i, distmat in enumerate(self.distmats):
# convert distmatrix to summon Matrix
if isinstance(distmat, matrix.Matrix):
mat = distmat
else:
mat = matrix.Matrix()
mat.from2DList(distmat)
# set default colormap
if mat.colormap == None:
mat.colormap = self.matrix_colormap
# determine labels
if self.dist_labels_from_align and self.align_order != None:
# determine row/col labels from alignment if it exists
mat.rowlabels = self.align_order
mat.collabels = self.align_order
elif self.distlabels != None:
mat.rowlabels = self.distlabels[i]
mat.collabels = self.distlabels[i]
else:
raise Exception("no labels given for matrix")
# reorder according to any given tree
if self.order != None:
lookup = util.list2lookup(mat.rowlabels)
mat.rperm = util.mget(lookup, self.order)
mat.cperm = util.mget(lookup, self.order)
mat.setup()
self.matrices.append(mat)
if self.seqs == None:
seqs = self.current_align
else:
seqs = self.seqs
# create matrix vis
self.current_matrix = self.matrices[0]
self.visdist = distmatrixvis.DistMatrixViewer(self.current_matrix,
seqs=seqs,
bgcolor=(1,1,1))
else:
self.visdist = None
开发者ID:Open-Technology,项目名称:Computational-Biology,代码行数:57,代码来源:phylovis.py
示例4: walk
def walk(node):
if node.isLeaf():
return smap(node.name)
else:
child_hashes = map(walk, node.children)
ind = util.sortrank(child_hashes)
child_hashes = util.mget(child_hashes, ind)
node.children = util.mget(node.children, ind)
return hash_tree_compose(child_hashes)
开发者ID:sarab609,项目名称:scraps,代码行数:9,代码来源:phylo.py
示例5: find_orthologs
def find_orthologs(gtree, stree, recon, counts=True):
"""Find all ortholog pairs within a gene tree"""
events = label_events(gtree, recon)
orths = []
for node, event in events.items():
if event == "spec":
leavesmat = [x.leaves() for x in node.children]
sp_counts = [util.hist_dict(util.mget(recon, row))
for row in leavesmat]
for i in range(len(leavesmat)):
for j in range(i+1, len(leavesmat)):
for gene1 in leavesmat[i]:
for gene2 in leavesmat[j]:
if gene1.name > gene2.name:
g1, g2 = gene2, gene1
a, b = j, i
else:
g1, g2 = gene1, gene2
a, b = i, j
if not counts:
orths.append((g1.name, g2.name))
else:
orths.append((g1.name, g2.name,
sp_counts[a][recon[g1]],
sp_counts[b][recon[g2]]))
return orths
开发者ID:sarab609,项目名称:scraps,代码行数:31,代码来源:phylo.py
示例6: lookup
def lookup(self, *keys, **options):
"""Returns a lookup dict based on a column 'key'
or multiple keys
extra options:
default=None
uselast=False # allow multiple rows, just use last
"""
options.setdefault("default", None)
options.setdefault("uselast", False)
lookup = util.Dict(dim=len(keys), default=options["default"])
uselast = options["uselast"]
for row in self:
keys2 = util.mget(row, keys)
ptr = lookup
for i in xrange(len(keys2) - 1):
ptr = lookup[keys2[i]]
if not uselast and keys2[-1] in ptr:
raise Exception("duplicate key '%s'" % str(keys2[-1]))
ptr[keys2[-1]] = row
lookup.insert = False
return lookup
开发者ID:sarab609,项目名称:scraps,代码行数:25,代码来源:tablelib.py
示例7: test_ml_large
def test_ml_large(self):
"""Test ML code"""
# params
bgfreq = [.258,.267,.266,.209]
kappa = 1.59
# data
tree = treelib.readTree("test/data/verts/19520/19520.ensembl.tree")
align = fasta.readFasta("test/data/verts/19520/19520.nt.mfa")
likes = []
dists = []
nodes = sorted(tree.nodes.values(), key=lambda x: x.dist)
l = spidir.calc_seq_likelihood_hky(tree, align, bgfreq, kappa)
print l
self.assert_(l != -util.INF)
l = spidir.find_ml_branch_lengths_hky(
tree,
util.mget(align, tree.leafNames()),
bgfreq, kappa,
parsinit=False,
maxiter=1)
print l
self.assert_(l != -util.INF)
开发者ID:Watermelon876,项目名称:spimap,代码行数:30,代码来源:ml.py
示例8: fit_distrib
def fit_distrib(cdf, params_init, data, ndivs=20, minsamples=5,
start=-util.INF, end=util.INF):
import scipy
import scipy.optimize
import scipy.stats
# determine ndiv and binsize
binsize = len(data) / ndivs
if binsize < minsamples:
ndivs = len(data) / minsamples
binsize = len(data) / ndivs
data = sorted(data)
bins = [data[i:i+binsize] for i in xrange(0, len(data), binsize)]
obs = scipy.array(map(len, bins))
ind = util.find(lambda x: x[-1] >= start and x[0] <= end, bins)
obs = util.mget(obs, ind)
def optfunc(params):
x = [bin[0] for bin in bins]
expected = [len(data) * cdf(x[1], params)]
expected.extend([len(data) *
(cdf(x[i+1], params) - cdf(x[i], params))
for i in range(1, len(x)-1)])
expected.append(len(data) * (1.0 - cdf(x[-1], params)))
expected = scipy.array(util.mget(expected, ind))
chi2, pval = scipy.stats.chisquare(obs, expected)
return chi2
params = scipy.optimize.fmin(optfunc, params_init, disp=False)
chi2, pval = chi_square_fit(cdf, params, data, ndivs, minsamples)
return list(params), pval
开发者ID:jeffhsu3,项目名称:argweaver,代码行数:35,代码来源:stats.py
示例9: _test_ml_speed
def _test_ml_speed(self):
# params
bgfreq = [.258,.267,.266,.209]
kappa = 1.59
# data
tree = treelib.readTree("test/data/flies.nt/0/0.tree")
align = fasta.readFasta("test/data/flies.nt/0/0.align")
likes = []
dists = []
nodes = sorted(tree.nodes.values(), key=lambda x: x.dist)
util.tic("find ML")
for i in xrange(10):
l = spidir.find_ml_branch_lengths_hky(
tree,
util.mget(align, tree.leafNames()),
bgfreq, kappa,
maxiter=10)
util.toc()
dists.append([n.dist for n in nodes])
likes.append(l)
开发者ID:Watermelon876,项目名称:spimap,代码行数:27,代码来源:ml.py
示例10: read_length_matrix
def read_length_matrix(filename, minlen=.0001, maxlen=1.0,
nooutliers=True):
"""Read a length matrix made by spidir-prep"""
from rasmus import util
dat = [line.rstrip().split("\t") for line in open(filename)]
species = dat[0][2:]
lens = util.map2(float, util.submatrix(dat, range(1, len(dat)),
range(2, len(dat[0]))))
gene_sizes = map(int, util.cget(dat[1:], 1))
files = util.cget(dat[1:], 0)
if nooutliers:
treelens = map(sum, lens)
m = mean(treelens)
ind = util.find(lambda x: x<5*m, treelens)
files, gene_sizes, lens, treelens = [util.mget(x, ind) for x in
files, gene_sizes, lens, treelens]
for row in lens:
for i in xrange(len(row)):
if row[i] < minlen:
row[i] = minlen
return species, lens, gene_sizes, files
开发者ID:Watermelon876,项目名称:dlcoal,代码行数:29,代码来源:__init__.py
示例11: on_reorder_leaves
def on_reorder_leaves(self):
leaves = self.current_tree.leaf_names()
# reorder matrix
for mat in self.matrices:
lookup = util.list2lookup(mat.rowlabels)
mat.rperm = util.mget(lookup, leaves)
mat.cperm = util.mget(lookup, leaves)
mat.setup()
if self.visdist:
self.visdist.redraw()
# reorder alignment
for aln in self.aligns:
aln.names = leaves
if self.visalign:
self.visalign.show()
开发者ID:Open-Technology,项目名称:Computational-Biology,代码行数:18,代码来源:phylovis.py
示例12: parsimony_C
def parsimony_C(aln, tree):
ptree, nodes, nodelookup = makePtree(tree)
leaves = [x.name for x in nodes if isinstance(x.name, str)]
seqs = util.mget(aln, leaves)
dists = pyspidir.parsimony(ptree, seqs)
for i in xrange(len(dists)):
nodes[i].dist = dists[i]
开发者ID:sarab609,项目名称:scraps,代码行数:9,代码来源:__init__.py
示例13: mlhkydist_C
def mlhkydist_C(aln, tree, bgfreq, ratio, maxiter):
ptree, nodes, nodelookup = makePtree(tree)
leaves = [x.name for x in nodes if isinstance(x.name, str)]
seqs = util.mget(aln, leaves)
dists, logl = pyspidir.mlhkydist(ptree, seqs, bgfreq, ratio, maxiter)
for i in xrange(len(dists)):
nodes[i].dist = dists[i]
return logl
开发者ID:sarab609,项目名称:scraps,代码行数:11,代码来源:__init__.py
示例14: draw_matches
def draw_matches(self, sp, chrom, start, end, drawn=None):
vis = []
if drawn is None:
drawn = set()
# build list of matches in order of drawing
for gene in iter_chrom(self.db.get_regions(sp, chrom), start, end):
# need to sort matches by genome order so that mult-genome synteny
# is drawn top-down
# get orthologs
genes2 = [x for x in self.orth_lookup.get(gene.data["ID"], [])
if x in self.region_layout]
if len(genes2) == 0:
continue
rows = util.groupby(lambda x: self.region_layout[x].y, genes2)
keys = util.sort(rows.keys(), reverse=True)
rows = util.mget(rows, keys)
l = self.region_layout
for i in range(1, len(rows)):
for botGene in rows[i]:
gene1 = self.db.get_region(botGene)
for topGene in rows[i-1]:
if (botGene, topGene) in drawn:
continue
drawn.add((botGene, topGene))
gene2 = self.db.get_region(topGene)
y1 = l[topGene].y
y2 = l[botGene].y + 1
x1 = l[topGene].x
x2 = l[topGene].x + gene2.length()
x3 = l[botGene].x + gene1.length()
x4 = l[botGene].x
if self.fat_matches:
vis.append(quads(
self.colors["matches"],
x1, y1,
x2, y1,
x3, y2,
x4, y2))
vis.append(lines(self.colors["matches"],
x1, y1,
x4, y2))
return group(* vis)
开发者ID:Open-Technology,项目名称:Computational-Biology,代码行数:54,代码来源:syntenyvis.py
示例15: optfunc
def optfunc(params):
x = [bin[0] for bin in bins]
expected = [len(data) * cdf(x[1], params)]
expected.extend([len(data) *
(cdf(x[i+1], params) - cdf(x[i], params))
for i in range(1, len(x)-1)])
expected.append(len(data) * (1.0 - cdf(x[-1], params)))
expected = scipy.array(util.mget(expected, ind))
chi2, pval = scipy.stats.chisquare(obs, expected)
return chi2
开发者ID:jeffhsu3,项目名称:argweaver,代码行数:11,代码来源:stats.py
示例16: _test_ml
def _test_ml(self):
"""Test ML code"""
# params
bgfreq = [.258,.267,.266,.209]
kappa = 1.59
# data
tree = treelib.readTree("test/data/flies.nt/0/0.tree")
align = fasta.readFasta("test/data/flies.nt/0/0.align")
likes = []
dists = []
nodes = sorted(tree.nodes.values(), key=lambda x: x.dist)
util.tic("find ML")
for i in range(40):
l = spidir.find_ml_branch_lengths_hky(
tree,
util.mget(align, tree.leafNames()),
bgfreq, kappa,
parsinit=False,
maxiter=1)
dists.append([n.dist for n in nodes])
likes.append(l)
util.toc()
print likes
prep_dir("test/output/ml/")
# distances plot
util.rplot_start("test/output/ml/ml_branches.pdf")
util.rplot("plot", util.cget(dists, 0),
ylim=[0, max(dists[0])], t="l",
main="branch length convergence",
xlab="iterations",
ylab="branch lengths (sub/site)")
for d in zip(* dists):
util.rplot("lines", d)
util.rplot_end(True)
print util.cget(dists, 4)
# likelihood plot
util.rplot_start("test/output/ml/ml_likelihood.pdf")
util.rplot("plot", likes, t="l",
xlab="iterations",
ylab="log likelihood",
main="likelihood convergence")
util.rplot_end(True)
开发者ID:Watermelon876,项目名称:spimap,代码行数:54,代码来源:ml.py
示例17: chiSquareFit
def chiSquareFit(xbins, ybins, func, nsamples, nparams, minsamples=5):
sizes = [xbins[i+1] - xbins[i] for i in xrange(len(xbins)-1)]
sizes.append(sizes[-1]) # NOTE: assumes bins are of equal size
# only focus on bins that are large enough
counts = [ybins[i] * sizes[i] * nsamples for i in xrange(len(xbins)-1)]
expected = []
for i in xrange(len(xbins)-1):
expected.append((func(xbins[i]) + func(xbins[i+1]))/2.0 *
sizes[i] * nsamples)
# ensure we have enough expected samples in each bin
ind = util.find(util.gefunc(minsamples), expected)
counts = util.mget(counts, ind)
expected = util.mget(expected, ind)
if len(counts) == 0:
return [0, 1], counts, expected
else:
return chiSquare([counts], [expected], nparams), counts, expected
开发者ID:jeffhsu3,项目名称:argweaver,代码行数:21,代码来源:stats.py
示例18: query_point_regions
def query_point_regions(point, regions, inc=True):
ind = util.sortindex(regions, key=lambda r: r[1])
rind = util.mget(range(len(regions)), ind)
regions_by_end = util.mget(regions, ind)
end = util.binsearch([r[0] for r in regions], x)[1]
start = util.binsearch([r[1] for r in regions_by_end], x)[0]
if start is None:
start = 0
if end is None:
end = len(regions)
if inc:
for i in xrange(start, end):
if regions[i][0] <= x <= regions[i][1]:
yield regions[i]
else:
for i in xrange(start, end):
if regions[i][0] < x < regions[i][1]:
yield regions[i]
开发者ID:alex-ozdemir,项目名称:phylogenetic-reconciliation,代码行数:22,代码来源:intervals.py
示例19: walk
def walk(node):
if node in leaves:
colors[node] = phylo.hash_tree(node, gene2species)
else:
# recurse
for child in node.children:
walk(child)
childHashes = util.mget(colors, node.children)
if len(childHashes) > 1 and util.equal(*childHashes):
nmirrors[0] += 1
childHashes.sort()
colors[node] = phylo.hash_tree_compose(childHashes)
开发者ID:mdrasmus,项目名称:dlcoal,代码行数:14,代码来源:topology_prior.py
示例20: make_pep_colors
def make_pep_colors(prop2color=prop2color):
pep_colors = util.Dict(default=color(.5, .5, .5))
AA = 'ARNDCEQGHILKMFPSTWYVU*'
pep_per_prop = util.hist_dict(util.mget(seqlib.AA_PROPERTY, AA))
prop_counts = util.Dict(default=0)
for char in AA:
prop = seqlib.AA_PROPERTY[char]
tint = prop_counts[prop] / float(pep_per_prop[prop])
pep_colors[char] = prop2color(prop, tint * .5)
prop_counts[prop] += 1
return pep_colors
开发者ID:Open-Technology,项目名称:Computational-Biology,代码行数:14,代码来源:genomebrowser.py
注:本文中的rasmus.util.mget函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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