Saravanan666/pypi-org huggingface dataset:
Package: cfv
cfv – Command-line File Verifycfv is a utility to test and create a wide range of checksum verification files.
It currently supports testing and creating sfv, sfvmd5, csv, csv2, csv4, md5, bsdmd5, sha1, sha224,
sha256, sha384, sha512, torrent and crc files.
Test-only support is available for par, par2.cfv was originally written by Matthew Mueller (original project home).
This is afriendly fork of cfvmaintained by David Gnedt.RequirementsPython ≥ 3.5 – older versions might work, but are unsupported.
For Python 2 support, see thepython2 branch.OptionalPython Imaging Library (PIL)orPillow– only needed if you want to create the
dimensions column of .crc files.InstallYou can get the latest releases via thePython Package Index (PyPI)or from theGithub releases page.
Other distribution ways are work-in-progress, seeissue #4.From PyPIIf you have a working Python installation with pip, you can follow these installation steps:pip install cfvread man pageman cfvor read usagecfv -hand have fun ☺️From SourceDownload a snapshot from theGithub releases pageor checkout the development version via Git.python setup.py installread man pageman cfvor read usagecfv -hand have fun ☺️optional: run tests to verify correct operation:cd test; ./test.pyContributionsContributions are welcome, just open a pull request ☺️Alternative ToolsHere is a community-compiled list of alternative tools that cover some of cfv's functionality (without warranty):GNU coreutils *sum: md5sum, sha1sum, sha224sum, sha256sum, sha384sum, sha512sum, ...cksfvrhash(with-rcdoes more or less the same thing as cfv, performance is good and it supports most hash formats including bittorrent. It lacks cfv's-mthough.)aria2c (to verify torrent checksums)bsdsfv (limited to 1024 files for some reason)pure-sfv (doesn't seem to display progress information, even with-v)bcfv(a Bash frontend to checksum programs (SHA, Blake3, MD5))CopyingThis program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
See the fileCOPYINGfor more information.
Package: cfwafenabler
cfwafenablerCloudFlare doesn't allow to set their entire WAF in Simulate mode. Instead, they suggest you to use the API.
cfwafenabler allows you to mass-modify all the rules to put your WAF in Simulate modeInstallationTo install cfwafenabler just usepipxpipx install cfwafenablerUsageBefore executing cfwafenabler, you need to set some CloudFlare environment variables.
If you use API key ( global permissions ) you need to set:export CF_API_EMAIL=your@email.com
export CF_API_KEY=YouApiKeyIf you are using CloudFlare API tokens, you only need to set (it's the same env variable, they reuse it):export CF_API_KEY=YouApiTokenThis token needs the following permissions:Zone.Zone:Read, Zone.Firewall Services:EditCreditsBased incanozokur'swork.This package was created withCookiecutterand thebyt3bl33d3r/pythoncookieproject template.
Package: cfwatch
Automagically purges CloudFlare’s cache when local files are updated.This is useful for exporting a directory of files via CloudFlare. If
your files are updated,cfwatchwill automatically purge the
corresponding URL on CloudFlare.Withcfwatch, you will no longer need to add cache busting query
strings, and the direct link will always work.Usage$ pip install cfwatch
$ cfwatch --help
usage: cfwatch.py [-h] [-l LOG] zone prefix [dir]

Purges CloudFlare on local file change.

positional arguments:
  zone               CloudFlare zone (e.g. example.com)
  prefix             CloudFlare path prefix (e.g. http://example.com/)
  dir                directory to watch, i.e. file.txt this directory is
                     http://example.com/file.txt

optional arguments:
  -h, --help         show this help message and exit
  -l LOG, --log LOG  log fileWhen runningcfwatch, you must set the following environment variables:CFWATCH_TOKENto your CloudFlare API token (not the legacy API key)
Package: cfx-address
cfx-addressConflux base32 address utilitiesFull documentation ->https://conflux-fans.github.io/cfx-address/cfx_address.html#module-cfx_addressinstallationpipinstallcfx-addressuse Base32Address class methodsfromcfx_addressimportBase32Addressvalidate a base32 addressBase32Address.is_valid_base32("0x1ecde7223747601823f7535d7968ba98b4881e09")# FalseBase32Address.validate("0x1ecde7223747601823f7535d7968ba98b4881e09")# will raise an exceptionencode and decode# encode hex address to base32Base32Address.encode_base32("0x1ecde7223747601823f7535d7968ba98b4881e09",network_id=1)#'cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4'# decode base32 addressBase32Address.decode("cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4")# result:# {'network_id': 1,# 'hex_address': '0x1ecde7223747601823f7535d7968ba98b4881e09',# 'address_type': 'user'}utilitiesaddress_str="cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4"address_verbose_str="CFXTEST:TYPE.USER:AATP533CG7D0AGBD87KZ48NJ1MPNKCA8BE1RZ695J4"assertBase32Address.equals(address_str,address_verbose_str)Base32Address.calculate_mapped_evm_space_address(address_str)Base32Address.zero_address(network_id=1)Base32Address.shorten_base32_address(address_str)Base32Address instancesinstance initializationaddress=Base32Address("cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4")# 'cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4'# Base32Address inherits from strassertisinstance(address,str)# init from hex address, in which case network_id is requiredBase32Address("0x1ecde7223747601823f7535d7968ba98b4881e09",network_id=1029)# 'cfx:aatp533cg7d0agbd87kz48nj1mpnkca8be7ggp3vpu'# change a base32 address to other networkBase32Address(address,network_id=1029)# 'cfx:aatp533cg7d0agbd87kz48nj1mpnkca8be7ggp3vpu'# verbose option defaults to FalseBase32Address(address,verbose=True)# 'CFXTEST:TYPE.USER:AATP533CG7D0AGBD87KZ48NJ1MPNKCA8BE1RZ695J4'eqand properties# __eq__ is implemented, address in same network is treated equalassertaddress=="cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4"assertaddress=="CFXTEST:TYPE.USER:AATP533CG7D0AGBD87KZ48NJ1MPNKCA8BE1RZ695J4"assert"CFXTEST:TYPE.USER:AATP533CG7D0AGBD87KZ48NJ1MPNKCA8BE1RZ695J4"==addressassert"cfxtest:aatp533cg7d0agbd87kz48nj1mpnkca8be1rz695j4"==address# address in different network is not equalmainnet_address=Base32Address(address,1029)assertmainnet_address=="cfx:aatp533cg7d0agbd87kz48nj1mpnkca8be7ggp3vpu"assertnotaddress==mainnet_address# properties[address.address_type,address.network_id,address.hex_address,address.verbose_address,address.short,address.mapped_evm_space_address]# ['user',#  1,#  '0x1ECdE7223747601823f7535d7968Ba98b4881E09',#  'CFXTEST:TYPE.USER:AATP533CG7D0AGBD87KZ48NJ1MPNKCA8BE1RZ695J4',#  'cfxtest:aat...95j4',#  '0x349f086998cF4a0C5a00b853a0E93239D81A97f6',#  ]
Package: cf-xarray
cf-xarrayA lightweight convenience wrapper for using CF attributes on xarray objects.For example you can use.cf.mean("latitude")instead of.mean("lat")if appropriate attributes are set! This allows you to write code that does not require knowledge of specific dimension or coordinate names particular to a dataset.See more in theintroductory notebook.Try out our Earthcube 2021 Annual Meeting notebooksubmission.
Package: cfxdb
cfxdbis a Crossbar.io Python support package with core database access classes
written in native Python. The package allows direct in-memory data access from
Python programs (including Jupyter notebooks) to CrossbarFX edge node data:persisted WAMP event historypersisted router tracing dataXBR market maker transactions databaseXBR network backend databaseWAMP session cachecustom user, embedded object databasesCopyright (c) typedef int GmbH. Licensed under MIT.
WAMP, Crossbar.io and XBR are trademarks of Crossbar.io Technologies GmbH.
Package: cfx-middleware
CFX MiddlewareDescriptionCFX Middleware is a middleware platform designed to facilitate integration and communication between parser results systems and CMAuthorVictor DominguezInstallationTo install the package runpipinstallcfx_middlewareif you want a specific version usepipinstallcfx_middleware==versionUsageIn your py file you must call the packagefrom cfx_middleware import parser_resultand provide the parser result dict or JSON as parameterExamplefromcfx_middlewareimportparser_resultsuccess=parser_result({parser_result})ifsuccess:dosomethingLicenseThis project is licensed under the PCD License.ContributingContributions are welcome! If you'd like to contribute to CFX Middleware, please follow these steps:Fork the repository.Create a branch for your new feature (git checkout -b feature/new-feature).Make your changes and commit them (git commit -am 'Add new feature').Push the branch (git push origin feature/new-feature).Create a new pull request.
Package: cg
cgcgstands forClinical Genomics; a clinical sequencing platform underSciLifeLabIn this context,cgprovides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:HTTP REST for powering the web portal:clinical.scilifelab.seCLI for interactions on the command lineContributingPlease check out ourguide for contributing to cgInstallationCg written in Python 3.9+ and is available on thePython Package Index(PyPI).pipinstallcgIf you would like to install the latest development version, usepoetry.gitclonehttps://github.com/Clinical-Genomics/cgcdcg
poetryinstall
Package: cg3d-maya-casc
cg3d-maya-cascEasily bridge data between Maya and Cascadeur with this Maya Module.Youtube video on how to useInstallationNotes:
Python 3 is required for Maya 2022.The installation can be found under documents\maya\modules\If the tool gives you issues you can open the cascadeur.mod file in a text editor and replace the + to -, to avoid loading the tool.  You can also simply delete the cascadeur.mod file and folder.Drag & DropThe easiest way to install this application is to ...Click this File Link >maya_casc_installer.py< to download the installation python file.Drag-n-drop it from the browser into a maya-viewport.
This will automatically install all the dependencies without requiring admin privileges into your user-directory.Hit 'Install'.  If any pop-ups appear, say "yes" or "allow".  The installer will likely take 20+ seconds.when closing Maya for the first time after installing the scripts you'll likely see a question like this:(you can say 'yes' to the question)Revisions1.0.1
Bug fixes for Maya 2022
Package: cg4
cgSimple yet powerful code generator.
Make use of your shell as possiable as cg can.Pity, the name cg is taken by others.Compare to hygen, yo.yo is way too slow and complicated.hygen pollutes all template files, and only support ejs.What I only need:template is runable as normal prj. No more $placehold$ stuff.instinct command follows the folder path.respect .gitignore.quick project to template and vice versa.prompt available.API designwhich one you prefer?# no slash
cg js react oldkey:newkey :newkey2 @:destname 

# with slash
cg js/react oldkey:newkey :newkey2 @:destnameScenario1cgjsreactoldkey:newkey:newkey0:newkey1@:destnamecopy $CG_TMPLS/js/react to $PWD/destnamechange all names from oldkey to newkey,  from  CG_ARG__0 to newkey0 ,from  CG_ARG__1 to newkey12cgjsreactJust copy $CG_TMPLS/js/react to $PWD/app
Package: cga2121
Technicolor CGA2121 Gateway Scraper libraryThis is a library to use in order to scrape Technicolor Gateway CGA2121Installationpip install cga2121How to use itfrom cga2121 import Cga2121
    
gateway = Cga2121("192.168.0.1", "80", "user", "pass")
  
gateway.authenticate()
  
devices = gateway.get_device_modal()
Package: cgai-DD
cgai-DD介绍钉钉群机器人的python API接口安装教程pipinstallcgai-DD注意1.仅支持python32.发送的图片路径必须是网络路径3.发送的图片格式图必须是jpg格式使用案例importcgai_DDasddWEBHOOK='https://oapi.dingtalk.com/robot/send?access_token=xxxxxx'发送文本信息dd.sendMessage(WEBHOOK,'发送的内容')发送连接message_url=r'https://zhuanlan.zhihu.com/p/391348944'title='CGAI-time'text='cgai-time一个简单又实用的时间日期处理python库'pic_url='https://obohe.com/i/2021/08/06/ikclyn.jpg'dd.sendLink(WEBHOOK,message_url,title,text,pic_url)发送markdownpic_url='https://obohe.com/i/2021/08/06/e1qrsr.png'markdown="""## cgai-time一个简单又实用的时间日期处理python库体育老师再也不用担心我算不出时间了![img](https://obohe.com/i/2021/08/06/ikclyn.jpg)###### 帮助说明 [链接](https://zhuanlan.zhihu.com/p/391348944)"""title='cgai-time分享'dd.sendMarkdown(WEBHOOK,markdown,title)发送ActionCardmarkdown="""![img](https://obohe.com/i/2021/08/06/ikclyn.jpg)### cgai-time"""showTitle='cgai-time'singleTitle='阅读文章'url='https://zhuanlan.zhihu.com/p/391348944'dd.sendActionCard(WEBHOOK,markdown,showTitle,singleTitle,url,btnOrientation=1)btns=[{"title":'链接1',"actionURL":url},{"title":'链接2',"actionURL":url}]dd.sendActionsCard(WEBHOOK,markdown,showTitle,singleTitle,url,btns,btnOrientation=0)发送Freecardurl='https://zhuanlan.zhihu.com/p/391348944'pic_url='https://obohe.com/i/2021/08/06/ikclyn.jpg'links=[{"title":"标题1","messageURL":url,"picURL":pic_url},{"title":"标题2","messageURL":url,"picURL":pic_url}]dd.sendFreeCard(WEBHOOK,links)
Package: cgai-excel
cgai-excel介绍操作excel图片获取规定：图片必须以内嵌的形式插入到单元格当中图片格子中的文字将不会识别解析到获取的图片路径前以img:为标识，比如: img:C:\Temp\output\EXT\xl/media\image6.jpeg安装教程pipinstallcgai-excel使用说明仅支持python3fromcgai_excel.Handlerimportget_excel_datapath=r'F:\Temp\Q\excel_module.xlsx'data=get_excel_data(path,extract_dirpath='F:\Temp\Q\Atemp')
Package: cgai-io
cgai-io介绍一个简单轻量又快速的数据流操作python库支持跨平台，支持window文件以及目录的快速复制
支持文件及文件目录删除，支持目录删除保留原目录结构
支持文件及目录移动,重命名
支持文件及目录打包与解压zip安装教程pip install cgai-io快速上手1.复制文件fromcgai_io.Copyimportcopyfilesrc1=r'D:\MZ\bg.jpg'des1=r'D:\Temp\Test\bg.jpg'copyfile(src1,des1)2.复制文件目录fromcgai_io.Copyimportcopydirsrc2=r'D:\MZ'des2=r'D:\Temp\Test\MZ'copydir(src2,des2)3.删除文件及文件目录fromcgai_io.Deleteimportdelfile,deldir,delall# #删除文件# path = r'\\192.168.1.248\3d\temp\a\cmd_mac.py'# delfile(path)# #删除文件夹# path = r'D:\BaiduNetdiskDownload\AA'# deldir(path,keep_dir=True)  #保留空目录结构#无论文件或文件夹都直接删除# path = r'D:\BaiduNetdiskDownload\ktk_103024'# delall(path)4.官方案例importcgai_ioasci# #复制文件# src = r'D:\Temp\2.jpg'# des = r'D:\Temp\2_bak.jpg'# ci.copyfile(src,des)# #复制文件目录# src = r'D:\Temp\AA'# des = r'D:\Temp\BB'# ci.copydir(src,des)# #删除文件# des = r'D:\Temp\2_bak.jpg'# ci.delfile(des)# # 删除文件目录# des = r'D:\Temp\BB'# ci.deldir(des)# # 删除文件或目录# des = r'D:\Temp\BB'# ci.delall(des)# #移动文件# src = r'D:\Temp\AA'# des = r'D:\Temp\BB'# ci.mvfile(src,des)# # 移动文件目录# src = r'D:\Temp\AA'# des = r'D:\Temp\testA\AA'# ci.mvdir(src,des)# # 移动文件或目录# src = r'D:\Temp\testA\AA'# des = r'D:\Temp\AA'# ci.mv(src,des)# 重命名文件或目录# src = r'D:\Temp\AA\A.jpg'# des = r'D:\Temp\AA\B.jpg'# ci.rename(src,des)# src = r'D:\Temp\AA'# des = r'D:\Temp\BB'# ci.rename(src,des)# # 文件添加前缀# src = r'D:\Temp\BB\B.jpg'# prefix = 'img_'# ci.addPrefix(src,prefix)  # r'D:\Temp\BB\img_B.jpg'# # 文件目录添加前缀# src = r'D:\Temp\BB'# prefix = 'dir_'# ci.addPrefix(src,prefix) # r'D:\Temp\dir_BB'# # 文件添加尾缀# src =r'D:\Temp\dir_BB\img_B.jpg'# suffix = '_001'# ci.addSuffix(src,suffix) # D:\Temp\dir_BB\img_B_001.jpg# # 文件目录添加尾缀# src = r'D:\Temp\dir_BB'# suffix = '_v001'# ci.addSuffix(src,suffix)  # r'D:\Temp\dir_BB_v001'# # 文件打包zip# src = r'D:\Temp\dir_BB\img_B.jpg'# des = r'D:\Temp\dir_BB\B.zip'# ci.pack(src,des)# # 文件目录打包zip# src = r'D:\Temp\dir_BB'# des = r'D:\Temp\BB.zip'# ci.pack(src,des)# # 解压文件或目录# src_zip = r'D:\Temp\A\BB.zip'# des_dir = r'D:\Temp\A\C'# ci.unpack(src_zip,des_dir)交流方式WeChat : zxzxde / 360014296
Package: cgai-path
#cgai-path功能应用于CG行业的文件路径基本使用importosfromcgai_pathimportCGAIPATHp=r'C:\PyOut\Test\test_hiero\v001\musk_%04d.exr'cpath=CGAIPATH()# 判断提供的路径是否为序列result=cpath.isSequence(p)print(result)# ('C:\\PyOut\\Test\\test_hiero\\v001\\musk_', '%04d')ifresult:filename=cpath.get_filename(p)print(filename)# musk# 获取文件序列paths,missings=cpath.get_files(p)print(paths)# ['C:\\PyOut\\Test\\test_hiero\\v001\\musk_0001.exr',...,'C:\\PyOut\\Test\\test_hiero\\v001\\musk_0049.exr']print()print(missings)a=r'C:\PyOut\Test\test_hiero\v001\musk_0001.exr'# 获取文件名称filename=cpath.get_filename(a)print(filename)# musk_0001
Package: cgai-socket
cgai-socket介绍简单轻量又快速的socket服务与客户请求库，支持绑定自定义函数安装pip install cgai-socket使用说明server:fromcgai_socket.cgai_serverimportServerdeffunc1(data):print('func1',data)returnNonedeffunc2(data,_id,_name):print('func2:',_id,_name)returnNonedeffunc3(data,_id2,_name2):print('func2:',_id2,_name2)return'func2'HOST='192.168.53.3'PORT=24601BUFFER=20480call_backs={func1:None,func2:(1,'CGAI01'),func3:(2,'CGAI02')}server=Server(HOST,PORT,BUFFER,call_backs=call_backs)server.listening()client:fromcgai_socket.cgai_clientimportClientHOST='192.168.53.3'PORT=24601BUFFER=20480my_client=Client(HOST,PORT,BUFFER)msg={'a':1,'b':2,'c':3}result=my_client.send(msg)print('result:',result)回调函数的定义关于回调函数的定义格式：回调函数的目的就是与客户端传来的数据进行交互，因此在自定义回调函数时:
1.必须有占位形参data(名称可随意改)。
2.每个回调函数必须有一个返回值，该可以为空，当不为空时，成功执行回调函数后会将该值传回给客户端，实现即时通信的效果回调函数定义格式如下为：>>> def func(data,*args):
>>>     xxxx
>>>     return None其中data为占位形参，你可以直接把它当做已知的从客户端传送过来的数据来直接操作。假如我们知道从客户端传送的数据是{"a":1,"b":2}，那么我们可以如此创建回调函数来使用数据：>>> def myfunc(data,_id,_name):
>>>     if data:
>>>         print("my data : ",data)
>>>         print("a : ",data.get('a',None))
>>>         print("_id : ",_id)
>>>         print("_name : ",_name)
>>>         return None添加回调函数1.使用add_callback添加回调函数：使用add_callback添加回调函数时可以传入参数，但是不需要传入data。因为data是客户端传来的数据，
这里只是当中占位参数。例：
>>> from cgai_socket.cgai_server import Server
>>>
>>> def myfunc(data,_id,_name):
>>>     print(data.get('a',''))
>>>     print(_id,_name)
>>>     return None
>>>
>>> my_server = Server('192.168.1.88',24601,1024)
>>> my_id = 12
>>> my_name = 'CGAI'
>>> my_server.add_callback(myfunc,args=(my_id,my_name))
>>> my_server.listening()

如果还有其他回调函数需要添加，可以继续使用add_callback,比如：
>>> def func1(data):xxx return None
>>> def func2(data):xxx return None
>>> ...
>>> my_server.add_callback(func1)
>>> my_server.add_callback(func2)
>>> ...注意：只有当所有回调函数添加完成后，最后执行listening开启服务。初始化创建server时添加多个回调函数:在初始化server时，是可以直接一次性添加多个回调函数，使用关键字参数 call_backs,
call_backs是一个字典，它使用结构是:
>>> {func1_name:(func1_args),func2_name:(func2_args),...}

例：
>>> def func1(data):xxx return None
>>> def func2(data,_id,_name):xxx return None
>>> def func3(data,_id1,_name2):xxx return None
>>> call_backs = {func1:None,func2:(_id,_name),fun3:(_id1,_name2)}
>>> my_server = Server('192.168.1.88',24601,1024,call_backs=call_backs)后台运行servercgai-socket 支持使用threading模块实现后台运行服务importthreadingimporttimefromcgai_socket.cgai_serverimportServerdeffunc1(data):print('func1',data)return'收到'HOST='192.168.53.3'PORT=24602BUFFER=20480call_backs={func1:None}definit_server():server=Server(HOST,PORT,BUFFER,call_backs=call_backs)server.listening()if__name__=='__main__':start_time=time.time()t=threading.Thread(None,init_server)t.setDaemon(True)t.start()whileTrue:end_time=time.time()ifend_time-start_time>10:print('停止主程序')break交流方式wx: zxzxde
Package: cgal4py
cgal4py is a Python interface for using theCGALDelaunay triangulation classes in any number of dimensions. Triangulation in parallel is also supported using the algorithm described inPeterka, Morozov, & Phillips (2014). Documentation for cgal4py can be foundhere.Licensingcgal4py is released as open source software under a BSD license.RequirementsFor running in serial:Python 2.7C++14 compilerCythonCGALVersion 3.5 or higher is required for periodic triangulations in 3D and version 4.9 or higher is required for periodic triangulations in 2D.For running in parallel you will need the above plus:MPI (eitherMPICHorOpenMPI)mpi4pymultiprocessingcykdtreeInstallationFrom Source1. Clone the cgal4py package usingMercurial.$ hg clonehttps://[username]@bitbucket.org/[username]/cgal4pywhere[username]should be replaced with your Bitbucket username.
2. From the distribution directory, execute the install script.$ python setup.py installIf you do not have administrative privileges, add the flag--userto the above command and the package will be installed in youruser package directory.Who do I talk to?This package is currently maintained byMeagan Lang.
Package: cgap-higlass-data
higlass-dataPackage that creates data files for CGAP's Higlass browsersInstallationSimply runpip install cgap-higlass-datato install the package. You need at least Python 3.8.To develop this package, clone this repo, make surepoetryis installed on your system and runmake install.CommandsAfter installation the following commands can be run from the command line:Convert BED file to BW (bigWig) fileAssume you have a BED file of the form# HEADER LINE 1
# HEADER LINE 2
chr1	0	1024	.	423
chr1	1024	2048	.	32
chr1	2048	3072	.	734This BED file can be converted to a BW file with the following command# -i input BED file path
# -o output BW file path
# -a assembly (currently only 'hg38' is supported
# -l number of header lines in the BED file
convert-bed-to-bw -i ./PATH/input.bed \
                  -o ./PATH/output.bw \
                  -a hg38 \
                  -l 2Note that thebedGraphToBigWigmust be installed on your system for this to work. It can be installed via conda (conda install -c bioconda ucsc-bedgraphtobigwig). You can also download the binary here:http://hgdownload.soe.ucsc.edu/admin/exe/Create variant-level VCF for CGAP's cohort browserThis command creates a multiresolution VCF file that is compatible to CGAP's cohort browser. Typically, the input VCF will be VEP annotated and has at least the info fieldlevel_most_severe_consequence(which is one ofHIGH,LOW,MODERATE,MODIFIER) and an importance value that can ranks/sorts the variants. The info field that is used for that purpose can be set dynamically.# -i input VCF path
# -o output VCF path
# -c info field in the input VCF that ranks the variants
# -m maximal tile values per consequence. Controls how may variants are displayed at once and a certain zoom level
# -q quiet True / False. Toggles verbose output
# -w chromosome-wise True / False. Significantly less memory intensive, but slightly slower.
# -t index output. True / False. If true, the output vcf will be indexed.
create-cohort-vcf -i ./PATH/input.vcf \
                  -o ./PATH/output.vcf \
                  -c p_value_negative_log_10 \
                  -q TrueCreate coverage BED file from VCFCounts the number of variants in a 1024bp window and creates a BED file with the results.# -i input VCF path
# -o output VCF path
# -a assembly
# -q quiet True / False. Toggles verbose output
create-coverage-bed -i ./PATH/input.vcf \
                    -o ./PATH/output.bed \
                    -a hg38 \
                    -q True
Package: cga-py
cga_pycga_py is an implementation of conformal geometric algebra (CGA) for python.Currently still in heavy development.Installpip install cga-pyUsageAs PackageSee tutorial.pyA full documentation is still in progress.As Visualization ToolIn your console execute the following command.cga_py_vis.pyThis will open the visualization interface.
All relevant parameters can be adjusted.
After adjustment of the parameters do not forget to update the specific parameter groups
or best the whole application.A full documentation of this tool and its capabilities will follow.