本文整理汇总了Python中jcvi.formats.bed.Bed.extract方法的典型用法代码示例。如果您正苦于以下问题：Python Bed.extract方法的具体用法？Python Bed.extract怎么用？Python Bed.extract使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类jcvi.formats.bed.Bed的用法示例。
在下文中一共展示了Bed.extract方法的2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，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
# 需要导入模块: from jcvi.formats.bed import Bed [as 别名]
# 或者: from jcvi.formats.bed.Bed import extract [as 别名]
def __init__(self, fig, root, datafile, bedfile, layoutfile,
switch=None, tree=None, extra_features=None,
chr_label=True, loc_label=True, pad=.05, vpad=.015,
scalebar=False):
w, h = fig.get_figwidth(), fig.get_figheight()
bed = Bed(bedfile)
order = bed.order
bf = BlockFile(datafile)
self.layout = lo = Layout(layoutfile)
switch = DictFile(switch, delimiter="\t") if switch else None
if extra_features:
extra_features = Bed(extra_features)
exts = []
extras = []
for i in xrange(bf.ncols):
ext = bf.get_extent(i, order)
exts.append(ext)
if extra_features:
start, end, si, ei, chr, orientation, span = ext
start, end = start.start, end.end # start, end coordinates
ef = list(extra_features.extract(chr, start, end))
# Pruning removes minor features with < 0.1% of the region
ef_pruned = [x for x in ef if x.span >= span / 1000]
print >> sys.stderr, "Extracted {0} features "\
"({1} after pruning)".format(len(ef), len(ef_pruned))
extras.append(ef_pruned)
maxspan = max(exts, key=lambda x: x[-1])[-1]
scale = maxspan / .65
self.gg = gg = {}
self.rr = []
ymids = []
#vpad = .012 * w / h
for i in xrange(bf.ncols):
ext = exts[i]
ef = extras[i] if extras else None
r = Region(root, ext, lo[i], bed, scale, switch,
chr_label=chr_label, loc_label=loc_label,
vpad=vpad, extra_features=ef)
self.rr.append(r)
# Use tid and accn to store gene positions
gg.update(dict(((i, k), v) for k, v in r.gg.items()))
ymids.append(r.y)
for i, j in lo.edges:
for ga, gb, h in bf.iter_pairs(i, j):
a, b = gg[(i, ga)], gg[(j, gb)]
ymid = (ymids[i] + ymids[j]) / 2
Shade(root, a, b, ymid, fc="gainsboro", lw=0, alpha=1)
for ga, gb, h in bf.iter_pairs(i, j, highlight=True):
a, b = gg[(i, ga)], gg[(j, gb)]
ymid = (ymids[i] + ymids[j]) / 2
Shade(root, a, b, ymid, alpha=1, highlight=h, zorder=2)
if scalebar:
print >> sys.stderr, "Build scalebar (scale={})".format(scale)
# Find the best length of the scalebar
ar = [1, 2, 5]
candidates = [1000 * x for x in ar] + [10000 * x for x in ar] + \
[100000 * x for x in ar]
# Find the one that's close to an optimal canvas size
dists = [(abs(x / scale - .12), x) for x in candidates]
dist, candidate = min(dists)
dist = candidate / scale
x, y, yp = .2, .96, .005
a, b = x - dist / 2, x + dist / 2
lsg = "lightslategrey"
root.plot([a, a], [y - yp, y + yp], "-", lw=2, color=lsg)
root.plot([b, b], [y - yp, y + yp], "-", lw=2, color=lsg)
root.plot([a, b], [y, y], "-", lw=2, color=lsg)
root.text(x, y + .02, human_size(candidate, precision=0),
ha="center", va="center")
if tree:
from jcvi.graphics.tree import draw_tree, read_trees
trees = read_trees(tree)
ntrees = len(trees)
logging.debug("A total of {0} trees imported.".format(ntrees))
xiv = 1. / ntrees
yiv = .3
xstart = 0
ystart = min(ymids) - .4
for i in xrange(ntrees):
ax = fig.add_axes([xstart, ystart, xiv, yiv])
label, outgroup, tx = trees[i]
draw_tree(ax, tx, outgroup=outgroup, rmargin=.4, leaffont=11)
xstart += xiv
RoundLabel(ax, .5, .3, label, fill=True, fc="lavender", color="r")示例2: __init__
# 需要导入模块: from jcvi.formats.bed import Bed [as 别名]
# 或者: from jcvi.formats.bed.Bed import extract [as 别名]
def __init__(self, fig, root, datafile, bedfile, layoutfile,
switch=None, tree=None, extra_features=None,
chr_label=True, pad=.04):
w, h = fig.get_figwidth(), fig.get_figheight()
bed = Bed(bedfile)
order = bed.order
bf = BlockFile(datafile)
lo = Layout(layoutfile)
switch = DictFile(switch, delimiter="\t") if switch else None
if extra_features:
extra_features = Bed(extra_features)
exts = []
extras = []
for i in xrange(bf.ncols):
ext = bf.get_extent(i, order)
exts.append(ext)
if extra_features:
start, end, si, ei, chr, orientation, span = ext
start, end = start.start, end.end # start, end coordinates
ef = list(extra_features.extract(chr, start, end))
# Pruning removes minor features with < 0.1% of the region
ef_pruned = [x for x in ef if x.span >= span / 1000]
print >> sys.stderr, "Extracted {0} features "\
"({1} after pruning)".format(len(ef), len(ef_pruned))
extras.append(ef_pruned)
maxspan = max(exts, key=lambda x: x[-1])[-1]
scale = maxspan / .65
self.gg = gg = {}
self.rr = []
ymids = []
vpad = .012 * w / h
for i in xrange(bf.ncols):
ext = exts[i]
ef = extras[i] if extras else None
r = Region(root, ext, lo[i], bed, scale, switch,
chr_label=chr_label, vpad=vpad, extra_features=ef)
self.rr.append(r)
# Use tid and accn to store gene positions
gg.update(dict(((i, k), v) for k, v in r.gg.items()))
ymids.append(r.y)
for i, j in lo.edges:
for ga, gb, h in bf.iter_pairs(i, j):
a, b = gg[(i, ga)], gg[(j, gb)]
ymid = (ymids[i] + ymids[j]) / 2
Shade(root, a, b, ymid, fc="gainsboro", lw=0, alpha=1)
for ga, gb, h in bf.iter_pairs(i, j, highlight=True):
a, b = gg[(i, ga)], gg[(j, gb)]
ymid = (ymids[i] + ymids[j]) / 2
Shade(root, a, b, ymid, alpha=1, highlight=h, zorder=2)
if tree:
from jcvi.graphics.tree import draw_tree, read_trees
trees = read_trees(tree)
ntrees = len(trees)
logging.debug("A total of {0} trees imported.".format(ntrees))
xiv = 1. / ntrees
yiv = .3
xstart = 0
ystart = min(ymids) - .4
for i in xrange(ntrees):
ax = fig.add_axes([xstart, ystart, xiv, yiv])
label, outgroup, tx = trees[i]
draw_tree(ax, tx, outgroup=outgroup, rmargin=.4)
xstart += xiv
RoundLabel(ax, .5, .3, label, fill=True, fc="lavender", color="r")