Saravanan666/pypi-org huggingface dataset:
Package: baseqRNA
# DropRNA## Install baseq_dropsWe need python3 and a package called: baseq_drops, which could be installed by:pip install baseqdropsAfter install, you will have a runnable command `baseq-Drop`## Config fileThe pipeline need the following software or resources:+ `star`: STAR software, for fast alignment of RNA-Seq data;+ `samtools`: Sorting bam file;+ `whitelistDir`: The barcode whitelist files for indrop and 10X should be placed under whitelistDir.These files can be downloaded from XXX.+ `cellranger_ref_<genome>`: The key process of read alignment and tagging to genesare inspired and borrowed from the open source cellranger pipeline(https://github.com/10XGenomics/cellranger).The refernces of genome index and transcriptome can be downloadedfrom https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest.In the config file, the directory of cellrange references is named as `cellranger_<genome>`.While running command, the configures are recorded in the file called `config_drops.ini`:[Drops]samtools = /path/to/samtoolsstar = /path/to/STARwhitelistDir = /path/to/whitelist_file_directorycellranger_hg38 = /path/to/reference/refdata-cellranger-GRCh38-1.2.0/## Process Steps1. `Extract the Cell Barcode` Counting the number of each kinds of barcode; this will genrate a barcode_count.<sample>.csv;2. `Cell Barcode correction and filtering` Correcting the cell barcode with 1bp mismatch, filtering the barcode with min number of reads;3. `Split the reads of valid Cell Barcodes` The raw pair-end raw reads are splitted to 16 single end files for multiprocessing according to the 2bp prefix of barcode; For example, we will get: split.<sample>.<AA|AT|AC|AG...|GG>.fq4. `Star Alignment` Fastq files runs at the same time; The bam file sorted by sequence header is generated;5. `Reads tagging` Tagging the reads alignment position to the corresponding gene name6. `Genrating UMI table`## Run CommandThe main config is:+ `--config`: config file;+ `--genome/-g`: genome version;+ `--protocol`: [10X|indrop|dropseq]+ `--minreads`:  Minimum reads for a barcode+ `--name/-n` : Sample name+ `--fq1/-1`: Read 1+ `--fq2/-2`: Read 2+ `--top_million_reads`: How many million reads to use, mainly for testing pipeline with fraction of reads (default 1000)+ `--dir/-d`: output pathIf you config the: `cellranger_ref_hg38` you can run the following:baseqdrops run_pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 10000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./### For older version 10X resultsThe cell barcode length is 15 and UMI length is 5.baseqdrops run_pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 10000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./
Package: baseqSNV
# baseqSNVThis package wraps GATK4 and Mutect2 for predicting SNVs from genomic sequencing data.## Install baseqSNV
We need python3 and a package called: baseq_drops, which could be installed by:pip install baseqSNVAfter install, you will have a runnable commandbaseqSNVFor more detailed tutorial and information, please visithttp://wgs.beiseq.cn/document_snv/index.html.
Package: base-qualitest-package
This package is an automation infrastructure kit tool for GUI and API tests.
This package made by Qualitest-GroupPackage Capabilities:selenium e2e base - initiate driver, basic actions, proxy server, and moreAPI base - validation options, wrapper for API's requests [get, post, put, patch, delete]shared utilities - run tests in parallel, DB connections, JSON actions, and moreunit tests - test for every function for saving the infrastructure accuracyIn our next versions:API Protocols capabilities, schema test validation by API's requestsdevelop a mobile e2e base - initiate driver, basic actions, proxy serveradding GUI report and wrapper any function in the packagecode-less automation framework for web, mobile, and API platforms
This package is an automation infrastructure kit tool for GUI and API tests. This package made by Qualitest-GroupPackage Capabilities:
selenium e2e base - initiate driver, basic actions, proxy server, and more
API base - validation options, wrapper for API's requests [get, post, put, patch, delete]
shared utilities - run tests in parallel, DB connections, JSON actions, and more
unit tests - test for every function for saving the infrastructure accuracyIn our next versions:
API Protocols capabilities, schema test validation by API's requests
develop a mobile e2e base - initiate driver, basic actions, proxy server
adding GUI report and wrapper any function in the package
code-less automation framework for web, mobile, and API platformsExample diagram:This is an example showing the relationship between the packages.
Driver (Selenium) and Test(Pytest/Unitest) share 1 to many relationship -> 1 Driver can run multiple tests.
Package: baserip
BaseripBaserip is a tool for copying a single video title from a DVD whilst
transcoding it. The purpose of this is to make the video available
to devices you may have which do not have a DVD player.Baserip was created because Acidrip is no longer being maintained
and I found myself needing a DVD ripper.
The design of Baserip is heavily influenced by Acidrip.Baserip is, in fact, a simple front-end to Mplayer/Mencoder which is
itself a front-end to some video encoding and decoding libraries.INSTALLATIONUnpack the tarball and go into the top level directory. As root
type:python3 setup.py installThe installation directory is usually:
/usr/local/lib/python3.x/dist-utilsHere you will find Baserip. Within Baserip you will find a “share”
directory. In this there is a .desktop file and an icon. You can use
these to manually add an entry to your desktop menu system.REQUIREMENTSIn order to run Baserip you will need the following:Python3PyQt4pyudevmplayer/mencoderlsdvdlameHOW TO USE BASERIPPlease read the on-line documentation.Baserip - What’s NextI have been waiting for a fixed version of lsdvd to become available. With
the introduction of Ubuntu 14.10 this has been realized. Unfortunately both
mencoder and ffmpeg have been dropped in favour of avconv and libav.Version 0.2 of baserip will use avconv and this work is currently underway.
The libav library (and thus avconv) cannot read directly from a DVD drive so I have taken the decision to interface directly with libdvdread in order to present a data stream to avconv for processing. A side-effect of this is that there will no longer be a dependency on lsdvd but, as I am now working at a lower level, getting this code ready is going to take some time.I do have some code ready with a few enhancements above the 0.1 release including more output containers and more selection over the audio encoding and audio bit rate but because I cannot install ffmpeg along side libav I cannot test this code. If anyone is willing to test for me and maybe even fix any problems then I can release version 0.2 and thus the avconv based version will become version 0.3.If you are interested in helping out then please contact me at:geoff (at) electron dot me dot ukand I will send you the latest code (minus the libav work). If we can get this working satisfactorally then this will form the basis of version 0.2 and I will continue to work on version 0.3.
Package: baserowapi
baserowapiBaserow API is a high-level API wrapper designed to integrate seamlessly withBaserow, the open-source no-code database tool.DocumentationFor comprehensive details on how to usebaserowapi, refer to theofficial documentation.If you're eager to get started, jump straight to thequick start guide.For feedback, suggestions, or contributions, please see theFeedback and Contributions section.InstallationTo installbaserowapi, simply use pip:pip install baserowapiFeaturesEfficient API Calls: The Baserow class offers a streamlined way to make API requests.Robust Data Management: Manipulate and manage Baserow tables with ease using the Table and Row classes.Advanced Filtering: Employ Filter objects to efficiently retrieve data from tables.LicenseThis project is licensed under the GNU GENERAL PUBLIC LICENSE, version 3.DependenciesRequestspytz
Package: bases
Bases provides a customisable, parametric implementation of several common styles of Base-N encoding, covering all cases appearing in themultibase specification(except for proquints).ContentsInstallUsageBase encoding objectsEncodingDecodingCase/padding variationsCase sensitivity variationsCustom base encodingsAPIContributingLicenseInstallYou can install the latest release fromPyPIas follows:$pipinstall--upgradebasesUsageWe suggest you import bases as follows:>>> import basesBelow are some basic usage examples, to get you started: for detailed documentation, seehttps://bases.readthedocs.io/Base encoding objects>>> from bases import base32
>>> base32
FixcharBaseEncoding(
    StringAlphabet('ABCDEFGHIJKLMNOPQRSTUVWXYZ234567',
                   case_sensitive=False),
    pad_char='=', padding='include')Encoding>>> b = bytes([70, 98, 190, 187, 66, 224, 178])
>>> base32.encode(b)
'IZRL5O2C4CZA===='Decoding>>> s = 'IZRL5O2C4CZA===='
>>> base32.decode(s)
b'Fb\xbe\xbbB\xe0\xb2'
>>> list(base32.decode(s))
[70, 98, 190, 187, 66, 224, 178]Case/padding variations>>> b = bytes([70, 98, 190, 187, 66, 224, 178])
>>> base32.encode(b)
'IZRL5O2C4CZA===='
>>> base32lower = base32.lower()
>>> base32lower
FixcharBaseEncoding(
    StringAlphabet('abcdefghijklmnopqrstuvwxyz234567',
                   case_sensitive=False),
    pad_char='=', padding='include')
>>> base32lower.encode(b)
'izrl5o2c4cza===='
>>> base32nopad = base32.nopad()
>>> base32nopad.encode(b)
'IZRL5O2C4CZA'Case sensitivity variations>>> s = 'IZRL5O2C4CZA===='
>>> base32lower.decode(s)
b'Fb\xbe\xbbB\xe0\xb2'
>>> base32lower_casesensitive = base32lower.with_case_sensitivity(True)
>>> base32lower_casesensitive.decode(s)
bases.encoding.errors.NonAlphabeticCharError: Invalid character 'I'
encountered for alphabet StringAlphabet('abcdefghijklmnopqrstuvwxyz234567').Custom base encodings>>> base4 = bases.make("0123", kind="zeropad-enc", block_nchars=4)
>>> base4
ZeropadBaseEncoding(StringAlphabet('0123'), block_nchars=4)APIFor the full API documentation, seehttps://bases.readthedocs.io/ContributingPlease seeCONTRIBUTING.md.LicenseMIT © Hashberg Ltd.
Package: bases.py
Utility for converting numbers to/from different bases/alphabets. Common bases have convenience aliases (seehttps://github.com/belldandu/bases.py#usage&&https://github.com/belldandu/bases.py#api), but arbitrary/custom alphabets can be used.As most people have noticed pythons int() only supports one way base conversions.
e.g.( int(‘lol’,36) # 28101 ). Pythons format() also only supports conversion the other way up to base 16. This library was created to help those python programmers by providing a bases conversion system that works both ways, can use customized conversions and supports from base 2 all the way up to base 64 all in one library.
Package: basesqlmodel
basesqlmodelA very simple CRUD class for SQLModel! :sparkles:InstallationpipinstallbasesqlmodelUsageimportasynciofromsqlalchemy.ext.asyncioimportAsyncSession,create_async_enginefromsqlalchemy.ormimportsessionmakerfromsqlmodelimportFieldfrombasesqlmodelimportBaseengine=create_async_engine("sqlite+aiosqlite:///:memory:")SessionLocal=sessionmaker(engine,expire_on_commit=False,class_=AsyncSession)classPotato(Base,table=True):id:int=Field(primary_key=True)name:strasyncdefmain():# Create tablesasyncwithengine.begin()asconn:awaitconn.run_sync(Base.metadata.create_all)# Interact with the Potato tableasyncwithSessionLocal()assession:obj=awaitPotato.create(session,name="Potato")print(f"Potato created:{repr(obj)}")obj=awaitPotato.get(session,name="Potato")print(f"Potato retrieved:{repr(obj)}")awaitobj.update(session,name="Fake Potato")print(f"Potato updated:{repr(obj)}")awaitPotato.delete(session,name="Fake Potato")print(f"Potato deleted:{repr(obj)}")objs=awaitPotato.get_multi(session)print(f"Confirm that the database is empty:{objs}")asyncio.run(main())LicenseThis project is licensed under the terms of the MIT license.
Package: basestation
A library to interface with the Valve Index® Base Stations (also commonly referred to as ‘Lighthouse V2’) through BLE.
This lib mostly exists because homeasstant requires all code directly interfacing with hardware to be done through a seperate lib, but it can be used just fine as a standalone lib.FeaturesScan for nearby base stations.Power stations on/offRead power stateIdentify (make LED flash)DescriptionI will write a more extensive API doc when I have my homeassistant stuff going.
Package: basestation-ctrl
basestation-ctrlbasestation-ctrl - A python library and CLI to wake up / power down SteamVR (Lighthouse) Base Stations. It currently only works for base stations v2.Are you annoyed by the constant high-pitch noise in your room? Have you unplugged your base
stations and after repowering they are not in sleep mode anymore? Are you using SteamVR in
Windows but want to control your base stations in Linux? Then you’ve come to the right place.basestation-ctrl allows you to power down, wake up and scan for base stations.Tested on Arch Linux (2021-11-20) with Python 3.9.7 and SteamVR Base Station 2.0.Usage(Note: I recommend using pipx instead of pip)Option A: Clone this repo and install from there:git clone https://github.com/schlagenhauf/basestation-ctrl.git
pip install --user <path_to_repo>Option B: Install from PyPIpip install --user basestation-ctrlThen consultbasestation-ctrl --helpfor details.Examples$ sudo basestation-ctrl scan
aa:bb:cc:dd:ee:ff 11:22:33:44:55:66
$ basestation-ctrl wake aa:bb:cc:dd:ee:ff 11:22:33:44:55:66
$ basestation-ctrl sleep aa:bb:cc:dd:ee:ff 11:22:33:44:55:66ToDosDetect if Bluetooth interface is available and turned onAdd commands for identifying the base stations and printing their statusKnown Issuesroot (e.g.sudo) permissions are required for a scan. See:https://github.com/IanHarvey/bluepy/issues/313Hickups when trying to connect too oftenAboutbasestation-ctrl is based onlh2ctrlandbasestation.
Package: basetech
📦 setup.py (for humans)This repo exists to providean example setup.pyfile, that can be used
to bootstrap your next Python project. It includes some advanced
patterns and best practices forsetup.py, as well as some
commented–out nice–to–haves.For example, thissetup.pyprovides a$ python setup.py uploadcommand, which creates auniversal wheel(andsdist) and uploads
your package toPyPiusingTwine, without the need for an annoyingsetup.cfgfile. It also creates/uploads a new git tag, automatically.In short,setup.pyfiles can be daunting to approach, when first
starting out — even Guido has been heard saying, "everyone cargo cults
thems". It's true — so, I want this repo to be the best place to
copy–paste from :)Check out the example!Installationcdyour_project# Download the setup.py file:#  download with wgetwgethttps://raw.githubusercontent.com/navdeep-G/setup.py/master/setup.py-Osetup.py#  download with curlcurl-Ohttps://raw.githubusercontent.com/navdeep-G/setup.py/master/setup.pyTo DoTests via$ setup.py test(if it's concise).Pull requests are encouraged!More ResourcesWhat is setup.py?on Stack OverflowOfficial Python Packaging User GuideThe Hitchhiker's Guide to PackagingCookiecutter template for a Python packageLicenseThis is free and unencumbered software released into the public domain.Anyone is free to copy, modify, publish, use, compile, sell, or
distribute this software, either in source code form or as a compiled
binary, for any purpose, commercial or non-commercial, and by any means.
Package: base-template-cli
Base Template CLIOverviewCLI tool ofBase Template Repository.RequirementsToolVersionBase Template Repositoryor itsJapanese version^7.8.0 or ^6.8.0 (ja)You have to clone eitherbase_templateorbase_template_jarepo to your machine before using Base Template CLI.gitclonegit@github.com:haru52/base_template.git# orgitclonegit@github.com:haru52/base_template_ja.gitInstallationpipinstallbase-template-cliUsageUsage: base-template-cli [OPTIONS] COMMAND [ARGS]...Base Template CLI.Options:--version   Show the version and exit.-h, --help  Show this message and exit.Commands:apply  Apply (Copy) Base Template boilerplates to the destination repo.Usage: base-template-cli apply [OPTIONS]BASE_TEMPLATE_ROOT_PATHApply (Copy) Base Template boilerplates to the destination repo.Options:-d, --dst TEXT          Destination repo root path.-t, --target-dirs TEXT  Target directories to copy (e.g., .husky,.github/ISSUE_TEMPLATE). If you don't specify thisoption, this command copies all files of BaseTemplate to the destination repo. If you want tocopy only root files, use --only-root option.-r, --only-root         Copy only root directory files of Base Templaterepo.-l, --lang TEXT         Language of Base Template. `en` or `ja`.-h, --help              Show this message and exit.Updatepipinstall-Ubase-template-cliUninstallpipuninstallbase-template-cliVersioning policySemantic Versioning 2.0.0LicenseMITContributingContributing GuidelineDocumentationDocumentation | base_template_cliAuthorharu
Package: baseten
BasetenThis is the Python client forBasetenandBlueprint.InstallationInstall the latest version of thebasetenpackage:pipinstall--upgradebasetenBasetenBaseten is a hosted platform for building ML-powered applications. Build apps with auto-scaling, GPU access, CRON jobs, and serverless functions.Visit our official documentation for Baseten atdocs.baseten.co.BlueprintBlueprint is the model fine-tuning and serving infrastructure for developers. It's powered by Baseten infrastructure and uses the baseten PyPi package.Visit our official documentation for Blueprint atdocs.blueprint.baseten.co.
Package: basevar
Call variants from ultra low-pass WGS data.InstallationpipinstallbasevarQuick startCall variants from several bamfilesbasevarbasetype-Rreference.fasta\--regionschr11:5246595-5248428,chr17:41197764-41276135\--batch-count50\-I00alzqq6jw.bam\-I09t3r9n2rg.bam\-I0fkpl1p55b.bam\-I13dg1gvsfk.bam\-I17phildszl.bam\-I1dbpgqt0dq.bam\-I1kyws27hoc.bam\--output-vcftest.vcf.gz\--output-cvgtest.cvg.tsv.gz\--nCPU4&&echo"** 5 done **"Or call variants from bamlistbasevarbasetype-Rreference.fasta\--regionschr11:5246595-5248428,chr17:41197764-41276135\--batch-count50\-Lbamfile.list\--output-vcftest.vcf.gz\--output-cvgtest.cvg.tsv.gz\--nCPU4&&echo"** 5 done **"
Package: base-version-checker
Installpipinstallbase-version-checkerUsage.bumpversion.cfgThis file is highly recommended to get the most out of this tool.
Without it you may get varied mileage from this as a git hook & when using bump2version.
Here's a simplified example. Useversion_checker -e([bumpversion_cfg_example.txt]) for more details[bumpversion]
current_version = 0.0.3

[bumpversion:file:Readme.md]
search = version_checker-{current_version}-py3-none-any.whl
replace = version_checker-{new_version}-py3-none-any.whl

[bumpversion:file:setup.cfg]
search = version = {current_version}
replace = version = {new_version}

[bumpversion:file:version.txt]

[bumpversion:file:kustomize/base/service.yaml]

[bumpversion:file:openapi-spec.json]
search = "version": "{current_version}"
replace = "version": "{new_version}"

[bumpversion:file:pom.xml]
search = <version>{current_version}</version> <!--this comment helps bumpversion find my (and only my) version!-->
replace = <version>{new_version}</version> <!--this comment helps bumpversion find my (and only my) version!-->bump version cfg formatThis format is driven by bump2version:https://github.com/c4urself/bump2version/blob/master/README.mdI cannot assert that search & replace are regex compatibile, I would strongly recommend you stick to the above format.[bumpversion]: top level of bumpversion cfg, this is the base for version synchronizing etc.{current_version}: the checker & bump2version dryly replace this value with that reported at the top of the cfg{new_version}: only used by bump2version and is replaced by thepartupdate commanded (patch v minor v major)[bumpversion:file:<file>]: section declaring a hardcoded version is present in a particular filesearch: used by the checker and bumper to search for specific text other than the current_versionreplace: used by the bumper only. the raw text to replace thesearchtextversion_checker usage assuming a .bumpversion.cfg# to run manuallyversion_checker-hVERSION_BASE=origin/non-main-branchversion_checker# to see an example .bumpversion.cfgversion_checker--example-config# to install as pre-push git hookversion_checker-ipre-push# add & commit your files, push should throw errors if versions not in sync/updated# the errors should tell you to do something like the followingbump2versionpatch
bump2version--helpenvironment variablesA few configurations can be modified by environment variables:Environment VariableDefaultDescriptionVERSION_BASEorigin/main or origin/masterThe base branch/commit to check versions againstVERSION_HEADHEADThe current commit to check versions onREPO_PATH.The path to the git repoVERSION_FILE.bumpversion.cfgThe config file with version configs to parseVERSION_REGEX([0-9]+\.?){3}?(\-([a-z]+)\.(\d+))The version regex to search for,changes to this have not been tested much
Package: basewhat
basewhatA Python utility for encoding/decoding arbitrary-base numbers.Usage:>>> b16 = BaseWhat(base=16)
>>> b16.from_int(65535)
'FFFF'
>>> b16.to_int('DECAFBAD')
3737844653
>>> b32 = BaseWhat(digits="23456789ABCDEFGHJKLMNPQRSTUVWXYZ")
>>> b32.from_int(32767)
'ZZZ'
>>> b32.from_int(9223372036854775808)
'A222222222222'
>>> b32.to_int('1900MIXALOT')
Traceback (most recent call last):
...
ValueError: Not a valid base 32 numberProject home page:https://sr.ht/~paulbissex/Basewhat/Author: Paul Bissexpaul@bissex.net