معرفی شرکت ها

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

Chunk and scatter the regions in a bed or sequence dict file

ویژگی	مقدار
سیستم عامل	-
نام فایل	chunked-scatter-1.0.0
نام	chunked-scatter
نسخه کتابخانه	1.0.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Leiden University Medical Center
ایمیل نویسنده	sasc@lumc.nl
آدرس صفحه اصلی	https://github.com/biowdl/chunked-scatter
آدرس اینترنتی	https://pypi.org/project/chunked-scatter/
مجوز	MIT

# chunked-scatter and scatter-regions The `chunked-scatter` tool takes a bed file, fasta index, sequence dictionary or vcf file as input and divides the contigs/chromosomes into overlapping chunks of a given size. These chunks will then be placed in new bed files, one chromosomes per file. Small chromosomes will be put together to avoid the creation of thousands of files. The `scatter-regions` tool works in a similar way but with defaults and flags tuned towards creating genome scatters for GATK tools. ## Installation - Install using pip: `pip install chunked-scatter` - Install using conda: `conda install chunked-scatter` - This requires [conda with a bioconda channel]( http://bioconda.github.io/user/install.html#). ## Usage ### chunked-scatter ``` usage: chunked-scatter [-h] [-p PREFIX] [-S] [-P] [-c SIZE] [-m MINIMUM_BP_PER_FILE] [-o OVERLAP] INPUT Given a sequence dict, fasta index or a bed file, scatter over the defined contigs/regions. Each contig/region will be split into multiple overlapping regions, which will be written to a new bed file. Each contig will be placed in a new file, unless the length of the contigs/regions doesn't exceed a given number. positional arguments: INPUT The input file. The format is detected by the extension. Supported extensions are: '.bed', '.dict', '.fai', '.vcf', '.vcf.gz', '.bcf'. optional arguments: -h, --help show this help message and exit -p PREFIX, --prefix PREFIX The prefix of the ouput files. Output will be named like: <PREFIX><N>.bed, in which N is an incrementing number. Default 'scatter-'. -S, --split-contigs If set, contigs are allowed to be split up over multiple files. -P, --print-paths If set prints paths of the output files to STDOUT. This makes the program usable in scripts and worfklows. -c SIZE, --chunk-size SIZE The size of the chunks. The first chunk in a region or contig will be exactly length SIZE, subsequent chunks will SIZE + OVERLAP and the final chunk may be anywhere from 0.5 to 1.5 times SIZE plus overlap. If a region (or contig) is smaller than SIZE the original regions will be returned. Defaults to 1e6 -m MINIMUM_BP_PER_FILE, --minimum-bp-per-file MINIMUM_BP_PER_FILE The minimum number of bases represented within a single output bed file. If an input contig or region is smaller than this MINIMUM_BP_PER_FILE, then the next contigs/regions will be placed in the same file untill this minimum is met. Defaults to 45e6. -o OVERLAP, --overlap OVERLAP The number of bases which each chunk should overlap with the preceding one. Defaults to 150. ``` ### scatter-regions ``` usage: scatter-regions [-h] [-p PREFIX] [-S] [-P] [-s SCATTER_SIZE] INPUT Given a sequence dict, fasta index or a bed file, scatter over the defined contigs/regions. Creates a bed file where the contigs add up approximately to the given scatter size. positional arguments: INPUT The input file. The format is detected by the extension. Supported extensions are: '.bed', '.dict', '.fai', '.vcf', '.vcf.gz', '.bcf'. optional arguments: -h, --help show this help message and exit -p PREFIX, --prefix PREFIX The prefix of the ouput files. Output will be named like: <PREFIX><N>.bed, in which N is an incrementing number. Default 'scatter-'. -S, --split-contigs If set, contigs are allowed to be split up over multiple files. -P, --print-paths If set prints paths of the output files to STDOUT. This makes the program usable in scripts and worfklows. -s SCATTER_SIZE, --scatter-size SCATTER_SIZE The maximum size for the regions over which to scatter. If contigs are not split, and a contig is bigger than the maximum size, the contig will be placed in its own file. Default: 1000000000. ``` ## Examples ### bed file Given a bed file located at `/data/regions.bed`: ``` chr1 100 1000 chr1 2000 16000 chr2 5000 10000 ``` The command: ``` chunked-scatter -p /data/scatter_ -m 1000 -c 5000 /data/regions.bed ``` Will produce the following two output files: - `/data/scatter_0.bed`: ``` chr1 100 1000 chr1 2000 7000 chr1 6850 12000 chr1 11850 16000 ``` - `/data/scatter_1.bed`: ``` chr2 5000 10000 ``` ### dict file Given a dict file located at `/data/ref.dict`: ``` @SQ SN:chr1 LN:3000000 @SQ SN:chr2 LN:500000 ``` The command: ``` chunked-scatter -p /data/scatter_ /data/regions.bed ``` Will produce the following output file at `/data/scatter_0.bed`: ``` chr1 0 1000000 chr1 999850 2000000 chr1 1999850 3000000 chr2 0 500000 ```

نیازمندی

مقدار	نام
>=0.11.2	pysam

زبان مورد نیاز

مقدار	نام
>=3.6	Python

نحوه نصب

نصب پکیج whl chunked-scatter-1.0.0:

pip install chunked-scatter-1.0.0.whl

نصب پکیج tar.gz chunked-scatter-1.0.0:

pip install chunked-scatter-1.0.0.tar.gz