本文整理汇总了Python中jcvi.formats.sizes.Sizes.close方法的典型用法代码示例。如果您正苦于以下问题：Python Sizes.close方法的具体用法？Python Sizes.close怎么用？Python Sizes.close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.sizes.Sizes的用法示例。
在下文中一共展示了Sizes.close方法的1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: scaffold
# 需要导入模块: from jcvi.formats.sizes import Sizes [as 别名]
# 或者: from jcvi.formats.sizes.Sizes import close [as 别名]
def scaffold(args):
"""
%prog scaffold scaffold.fasta synteny.blast synteny.sizes synteny.bed
physicalmap.blast physicalmap.sizes physicalmap.bed
As evaluation of scaffolding, visualize external line of evidences:
* Plot synteny to an external genome
* Plot alignments to physical map
* Plot alignments to genetic map (TODO)
Each trio defines one panel to be plotted. blastfile defines the matchings
between the evidences vs scaffolds. Then the evidence sizes, and evidence
bed to plot dot plots.
This script will plot a dot in the dot plot in the corresponding location
the plots are one contig/scaffold per plot.
"""
from jcvi.graphics.base import set_image_options
from jcvi.utils.iter import grouper
p = OptionParser(scaffold.__doc__)
p.add_option("--cutoff", type="int", default=1000000,
help="Plot scaffolds with size larger than [default: %default]")
p.add_option("--highlights",
help="A set of regions in BED format to highlight [default: %default]")
opts, args, iopts = set_image_options(p, args, figsize="14x8", dpi=150)
if len(args) < 4 or len(args) % 3 != 1:
sys.exit(not p.print_help())
highlights = opts.highlights
scafsizes = Sizes(args[0])
trios = list(grouper(3, args[1:]))
trios = [(a, Sizes(b), Bed(c)) for a, b, c in trios]
if highlights:
hlbed = Bed(highlights)
for scaffoldID, scafsize in scafsizes.iter_sizes():
if scafsize < opts.cutoff:
continue
logging.debug("Loading {0} (size={1})".format(scaffoldID,
thousands(scafsize)))
tmpname = scaffoldID + ".sizes"
tmp = open(tmpname, "w")
tmp.write("{0}\t{1}".format(scaffoldID, scafsize))
tmp.close()
tmpsizes = Sizes(tmpname)
tmpsizes.close(clean=True)
if highlights:
subhighlights = list(hlbed.sub_bed(scaffoldID))
imagename = ".".join((scaffoldID, opts.format))
plot_one_scaffold(scaffoldID, tmpsizes, None, trios, imagename, iopts,
highlights=subhighlights)