本文整理匯總了Python中CGAT.Genomics.readContigSizes方法的典型用法代碼示例。如果您正苦於以下問題：Python Genomics.readContigSizes方法的具體用法？Python Genomics.readContigSizes怎麽用？Python Genomics.readContigSizes使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類CGAT.Genomics的用法示例。
在下文中一共展示了Genomics.readContigSizes方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: main
# 需要導入模塊: from CGAT import Genomics [as 別名]
# 或者: from CGAT.Genomics import readContigSizes [as 別名]
#.........這裏部分代碼省略.........
parser.set_defaults(
input_filename_contigs=False,
filename_crop_gff=None,
input_filename_agp=False,
genome_file=None,
add_up_flank=None,
add_down_flank=None,
complement_groups=False,
crop=None,
crop_unique=False,
ignore_strand=False,
filter_range=None,
min_distance=0,
max_distance=0,
min_features=1,
max_features=0,
extension_upstream=1000,
extension_downstream=1000,
sanitize_method="ucsc",
flank_method="add",
output_format="%06i",
skip_missing=False,
is_gtf=False,
group_field=None,
contig_pattern=None,
)
(options, args) = E.Start(parser, argv=argv)
contigs = None
genome_fasta = None
if options.input_filename_contigs:
contigs = Genomics.readContigSizes(
IOTools.openFile(options.input_filename_contigs, "r"))
if options.genome_file:
genome_fasta = IndexedFasta.IndexedFasta(options.genome_file)
contigs = genome_fasta.getContigSizes()
if options.method in ("forward_coordinates", "forward_strand",
"add-flank", "add-upstream-flank",
"add-downstream-flank") \
and not contigs:
raise ValueError("inverting coordinates requires genome file")
if options.input_filename_agp:
agp = AGP.AGP()
agp.readFromFile(IOTools.openFile(options.input_filename_agp, "r"))
else:
agp = None
gffs = GTF.iterator(options.stdin)
if options.method in ("add-upstream-flank",
"add-downstream-flank",
"add-flank"):
add_upstream_flank = "add-upstream-flank" == options.method
add_downstream_flank = "add-downstream-flank" == options.method
if options.method == "add-flank":
add_upstream_flank = add_downstream_flank = True
upstream_flank = int(options.extension_upstream)
downstream_flank = int(options.extension_downstream)
extend_flank = options.flank_method == "extend"