Saravanan666/pypi-org huggingface dataset:
Package: becas
becas-pythonis the official Python client for the becas API.becasis a biomedical concept annotator available through an HTTP API.This package allows usage of the becas API from a command-line tool or
programmatically from Python modules.Install it with:$ pip install becasAnd learn to use it by reading thedocumentation.copyright:2013, Tiago Nunes, Universidade de Aveirolicense:Creative Commons Attribution-NoncommercialResourcesDocumentationIssue TrackerCodebecas API documentationAbout becas
Package: bech32
bech32Since this implementation wasn't in a place that was easy to use for Python programmers I took it from fromhttps://github.com/rustyrussell/lightning-payencodeand publishedon GitHubandon PyPI.The original version of this package is probably the one athttps://github.com/sipa/bech32/tree/master/ref/python, but apparently Rusty Russel commented out the 90-length limit of bech32-encoded stuff so it could be used for Lightning invoices. Let's keep that change.Installpip install bech32
Package: bech32m-chia
bech32m_chia for pythonA BIP350 compatible Bech32m encoding/decoding library for chia.installpipinstallbech32m-chiaUseimportfrombech32m_chiaimportbech32mExampleprint(bech32m.encode("7382e99e0679b68b6e8211c48224c99fc941a5f035bd85f9f32c4a8f48d3bb29","xch"))print(bech32m.encode("0x7382e99e0679b68b6e8211c48224c99fc941a5f035bd85f9f32c4a8f48d3bb29","xch"))print(bech32m.encode("7382e99e0679b68b6e8211c48224c99fc941a5f035bd85f9f32c4a8f48d3bb29",""))print(bech32m.encode("7382e99e0679b68b6e8211c48224c99fc941a5f035bd85f9f32c4a8f48d3bb29","nft"))# xch1wwpwn8sx0xmgkm5zz8zgyfxfnly5rf0sxk7ct70n939g7jxnhv5smryxmv# xch1wwpwn8sx0xmgkm5zz8zgyfxfnly5rf0sxk7ct70n939g7jxnhv5smryxmv# xch1wwpwn8sx0xmgkm5zz8zgyfxfnly5rf0sxk7ct70n939g7jxnhv5smryxmv# nft1wwpwn8sx0xmgkm5zz8zgyfxfnly5rf0sxk7ct70n939g7jxnhv5sam5p80print(bech32m.decode("xch1wwpwn8sx0xmgkm5zz8zgyfxfnly5rf0sxk7ct70n939g7jxnhv5smryxmv"))# 7382e99e0679b68b6e8211c48224c99fc941a5f035bd85f9f32c4a8f48d3bb29SupportXCH:xch1crwg0ryz5rf90a6xmmspza2jmhc437sllnen8m7nu2dlx7ugjs9qaxgyjwpawket:hezuoshe.xch
Package: bechdel
IntroductionTheBechdelpackage wraps thebechdeltest.comAPI and allows users to
programmatically retrieve theBechdel
scorefor movies.You can search for movies either by title…importbechdelmovies=bechdel.getMoviesByTitle('terminator')len(movies)# 5printmovies[0]{u'date':u'2015-07-02 06:24:18',u'dubious':u'0',u'id':u'6340',u'imdbid':u'1340138',u'rating':u'0',u'submitterid':u'12302',u'title':u'Terminator Genisys',u'visible':u'1',u'year':u'2015'}…or by IMDb id:terminator_genisys=bechdel.getMovieByImdbId('1340138')DisclaimerThis package and its author are unaffiliated withbechdeltest.com. Please don’t abuse the API
with unnecessary requests.
Package: beckett
Hypermedia API Client FrameworkBeckett is a convention-based framework for building Python interfaces around HTTP APIs.📚 Documentationhttps://phalt.github.io/beckett📖 FeaturesDefine your API client in Python instead of a data serialization language.Encourages good HTTP and REST practices without being too strict.Resources are transformed into typed instances - no more raw dictionaries!Automatic URL routing for RESTful interaction to your resources.Hypermedia relationship links are automagically resolved into python methods.Supports hypermedia response formats such as JSONAPI and HAL. [IN DEV]Works out of the box, but each resource is completely configurable.🏗 StatusBeckett isstableand suitable for projects, but expect occasional updates for bug fixes.🎥 CreditsThis package was created withCookiecutter.We usePython Requestsfor talking HTTP.Free software: ISClicense
Package: bec-lib
BEC Libbec-lib is a Python library communicating with theBeamline and Experiment Control (BEC)server. It is primarily used to build new BEC clients such as graphical user interfaces (GUIs) or command line interfaces (CLIs).InstallationUse the package managerpipto install bec-lib.pipinstallbec-libDocumentationThe documentation is part of the BEC documentation and can be foundhere.Usagefrombec_libimportBECClient# Create a new BECClient instance and start itbec=BECClient()bec.start()# Convenient access to scans and devicesscans=bec.scansdev=bec.device_manager.devices# define a dummy callback functiondefdummy_callback(data,metadata):print(data,metadata)# add the callback and subscribe to the scan segmentsbec.callbacks.register(event_type="scan_segment",callback=dummy_callback,sync=False)ContributingMerge requests are very welcome! For major changes, please open an issue first to discuss what you would like to change.
All commits should use the Angular commit scheme:<type>(<scope>): <short summary>
  │       │             │
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  │       └─⫸ Commit Scope: animations|bazel|benchpress|common|compiler|compiler-cli|core|
  │                          elements|forms|http|language-service|localize|platform-browser|
  │                          platform-browser-dynamic|platform-server|router|service-worker|
  │                          upgrade|zone.js|packaging|changelog|docs-infra|migrations|ngcc|ve|
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  └─⫸ Commit Type: build|ci|docs|feat|fix|perf|refactor|testThe<type>and<summary>fields are mandatory, the(<scope>)field is optional.TypeMust be one of the following:build: Changes that affect the build system or external dependencies (example scopes: gulp, broccoli, npm)ci: Changes to our CI configuration files and scripts (examples: CircleCi, SauceLabs)docs: Documentation only changesfeat: A new featurefix: A bug fixperf: A code change that improves performancerefactor: A code change that neither fixes a bug nor adds a featuretest: Adding missing tests or correcting existing testsPlease make sure to update tests as necessary.LicenseBSD-3-Clause
Package: beCoditive
beCoditiveBugs and glitchesFeel free to report all bugs and glitches by creating an issue in theissue section.A correct and understandable issue contains :Steps to reproduceCode that summonned the errorThe complete errorYou can also join me on mydiscord server.ConfigurationThe first step is to import the module in your code.importbecoditiveclient=becoditive.API()Then you have to login and request a API call according to your choice.client.login("YOUR_BECODITIVE_API_KEY")print(client.cat())Available API Callsclient.dog()client.cat()client.panda()client.bird()client.uuid()client.joke()client.puns())client.hug()client.kiss()client.insults()client.flirt()client.word()client.doesnotexists()client.quote()client.uselessweb()client.truth()client.dare()client.number()client.password()
Package: bec-scan-server
BEC scan serverbec-scan-server is a core Python service for theBeamline and Experiment Control (BEC)server, tasked with the handling and orchestrating the data acquisition.InstallationUse the package managerpipto install bec-scan-server.pipinstallbec-scan-serverDocumentationThe documentation is part of the BEC documentation and can be foundhere.ContributingMerge requests are very welcome! For major changes, please open an issue first to discuss what you would like to change.
All commits should use the Angular commit scheme:<type>(<scope>): <short summary>
  │       │             │
  │       │             └─⫸ Summary in present tense. Not capitalized. No period at the end.
  │       │
  │       └─⫸ Commit Scope: animations|bazel|benchpress|common|compiler|compiler-cli|core|
  │                          elements|forms|http|language-service|localize|platform-browser|
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  └─⫸ Commit Type: build|ci|docs|feat|fix|perf|refactor|testThe<type>and<summary>fields are mandatory, the(<scope>)field is optional.TypeMust be one of the following:build: Changes that affect the build system or external dependencies (example scopes: gulp, broccoli, npm)ci: Changes to our CI configuration files and scripts (examples: CircleCi, SauceLabs)docs: Documentation only changesfeat: A new featurefix: A bug fixperf: A code change that improves performancerefactor: A code change that neither fixes a bug nor adds a featuretest: Adding missing tests or correcting existing testsPlease make sure to update tests as necessary.LicenseBSD-3-Clause
Package: bec-widgets
BEC WidgetsBEC Widgets is a GUI framework designed for interaction withBEC (Beamline Experiment Control).InstallationUse the package managerpipto install BEC Widgets:pipinstallbec-widgetsFor development purposes, you can clone the repository and install the package locally in editable mode:gitclonehttps://gitlab.psi.ch/bec/bec-widgetscdbec-widgets
pipinstall-e.[dev]BEC Widgets currently supports both PyQt5 and PyQt6. By default, PyQt6 is installed.To select a specific Python Qt distribution, install the package with an additional tag:pipinstallbec-widgets[pyqt6]orpipinstallbec-widgets[pyqt5]DocumentationDocumentation of BEC Widgets can be foundhere. The documentation of the BEC can be foundhere.ContributingAll commits should use the Angular commit scheme:Angular Commit Message Header<type>(<scope>): <short summary>
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  │       │             └─⫸ Summary in present tense. Not capitalized. No period at the end.
  │       │
  │       └─⫸ Commit Scope: animations|bazel|benchpress|common|compiler|compiler-cli|core|
  │                          elements|forms|http|language-service|localize|platform-browser|
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  │                          upgrade|zone.js|packaging|changelog|docs-infra|migrations|ngcc|ve|
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  └─⫸ Commit Type: build|ci|docs|feat|fix|perf|refactor|testThe<type>and<summary>fields are mandatory, the(<scope>)field is optional.TypeMust be one of the following:build: Changes that affect the build system or external dependencies (example scopes: gulp, broccoli, npm)ci: Changes to our CI configuration files and scripts (examples: CircleCi, SauceLabs)docs: Documentation only changesfeat: A new featurefix: A bug fixperf: A code change that improves performancerefactor: A code change that neither fixes a bug nor adds a featuretest: Adding missing tests or correcting existing testsLicenseBSD-3-Clause
Package: bed
A very simple command line Browser Extension DownloaderInstallationUsing git# clone the repo$gitclonehttps://github.com/sdushantha/bed.git# install the requirements$pip3install--user-rrequirements.txtUsing pipNote: I will uploadbedto pypi soonpip3 install --user git+https://github.com/sdushantha/bedUsageSupported browsersFirefoxChrome or any browser that uses the Chrome Web StoreOperausage:bed[-h]url

AverysimplecommandlineBrowserExtensionDownloader

positionalarguments:url

optionalarguments:-h,--helpshowthishelpmessageandexit
Package: bed2idt
bed2idtThis command-line interface (CLI) generates IDT input files from a 7-column primer bed file.DescriptionThe IDT Input File Generator CLI allows you to convert a primer bed file into IDT input files. IDT (Integrated DNA Technologies) is a company that provides custom DNA synthesis services. This tool automates the process of generating input files for ordering primers from IDT.InstallationFrom pippip instal bed2idtFrom Poetry / sourcegit clone https://github.com/ChrisgKent/bed2idtpoetry install && poetry buildUsageTo use the CLI, run the following command:bed2idt [options] [command] [command-options]OptionsThe CLI supports the following options:-b, --bedfile: Path to the primer bed file (required).-o, --output: The output location for the generated IDT input file(s) (default:output.xlsx).platecommand:-s, --splitby: Specifies whether the primers should be split across more than one plate. Valid options arepool,ref,none,nest(default:pool).-f, --fillby: Specifies how the plates should be filled. Valid options arerowsorcols(default:cols).--plateprefix: The prefix for the plate namestubecommand:-s, --scale: The concentration of the primers. Valid options are25nm,100nm,250nm,1um,2um,5um,10um,4nmU,20nmU,PU, or25nmS(default:25nm).-p, --purification: The purification method for the primers. Valid options areSTD,PAGE,HPLC,IEHPLC,RNASE,DUALHPLC, orPAGEHPLC(default:STD).--force: Overrides the output directory if it already exists.ExamplesGenerate 96-well plate IDT input files for a primer bed file namedprimer.bedand save/overide the output asoutput.xlsx, split by pools:bed2idt -b primer.bed --force plate --splitby poolsGenerate tube IDT input files for a primer bed file namedprimer.bed, save the output ascustom_output.xlsx, and specify a purification method:bed2idt -b primer.bed -o custom_output.xlsx tube --purification PAGEGenerate IDT input files for a primer bed file namedprimer.bedwithout splitting the primers across multiple plates:bed2idt -b primer.bed plate --splitby noneGenerate IDT input filesprimer.xlsxfor a primer.bed file namedprimer.bed, splitting the plate by pool, and filling plates by col:bed2idt -b primer.bed -o primer.xlsx plate  --splitby pools --filllby colsNote: Make sure to replacepythonwith the appropriate command for running Python on your system.
Package: be-datahive
be-datahivePython library for theBE-dataHIVE
API.Installationbe_datahiveis available onPYPI. Install withpip:pipinstallbe_datahiveDocumentationCreate anapiobject for interacting with the API:frombe_datahiveimportbe_datahiveapi=be_datahive()Obtain efficiency & bystander data:efficiency_data=api.get_efficiency()bystander_data=api.get_bystander()Convert efficiency & bystander data into machine-ready arrays:ef_features,ef_target=api.get_efficiency_ml_arrays(efficiency_data,encoding='one-hot')by_features,by_target=api.get_bystander_ml_arrays(bystander_data,encoding='one-hot')CitationWhen using theBE-dataHIVE
API, please cite our paper as outlined below.@article{Schneider.2023,title="BE-dataHIVE: a Base Editing Database",author="Lucas Schneider, Peter Minary",year="2023",}
Package: bedboss
bedbossbedboss is a command-line pipeline that standardizes and calculates statistics for genomic interval data, and enters the results into a BEDbase database. It has 3 components: 1) bedmaker (bedboss make); 2) bedqc (bedboss qc); and 3) bedstatbedboss stat. You may run all 3 pipelines separately, together (bedbase all).1) bedmakerConverts supported file types into BED and bigBed format. Currently supported formats:bedGraphbigBedbigWigwig2) bedqcAssess QC of BED files and flag potential problems for further evaluation so you can determine whether they should be included in downstream analysis.
Currently, it flags BED files that are larger than 2 GB, have over 5 milliom regions, or have mean region width less than 10 bp.
These thresholds can be changed with pipeline arguments.bedstatCalculates statistics about BED files.DocumentationDetailed information about each pipeline can be found in thebedboss Readme.For the specific bedbase.org instance, see instructions in the bedbase.org repo.
Package: beddit-python
API Client forBedditin Python.ReadAPI Documentationfor detail.Installationpipinstallbeddit-pythonUsageList sleep scores per dayfromdatetimeimportdatetimefrombeddit.clientimportBedditClientclient=BedditClient('user@example.com',password)start_date=datetime(2016,7,1)end_date=datetime(2016,7,31)sleeps=client.get_sleeps(start=start_date,end=end_date)forsleepinsleeps:print(sleep.date.strftime('%Y-%m-%d'),sleep.property.total_sleep_score)2016-07-01 75
2016-07-02 92
....Supported PythonPython 2.7, 3.3, 3.4, 3.5LICENSEMIT License
Package: bedhandler
BedhandlerBedhandler is a Python 3.x package for loading BED and TSV files related to Ion TorrentTMsequencers from ThermoFisher Scientific. For example,
the BED for amplicons, effective regions and the TSV file containing coverage data for a specific run.This package was created by the IP4-Team at Pele Pequeno Principe Research Institute and is under active maintenance and improvement.Install with pippip3 install bedhandler
Package: bedhost
bedhostbedhostis a Python FastAPI module for the API that powers BEDbase
It needs a path to thebedbase configuration file, which can be provided either via-c/--configargument or read from$BEDBASE_CONFIGenvironment variable.Running for developmentRunning withuvicornprovides auto-reload. To configure, this assumes you have previously set updatabio/secrets.Source.envfile to populate the environment variables referenced in the configuration file.Startbedhostusinguvicornand pass the configuration file via theBEDBASE_CONFIGenv var.source ../bedbase.org/environment/production.envBEDBASE_CONFIG=../bedbase.org/config/api.bedbase.org.yaml uvicorn bedhost.main:app --reloadYou can change the database you're connecting to by using a different config file:Using a local config:BEDBASE_CONFIG=../bbconf/tests/data/config.yaml uvicorn bedhost.main:app --reloadWith new database:BEDBASE_CONFIG=../bedbase.org/config/bedbase2.yaml uvicorn bedhost.main:app --reloadNow, you can access the service athttp://127.0.0.1:8000. Example endpoints:127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img/open_chromatin127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img_path/open_chromatin127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file/bedfile127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file_path/bedfile127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata?attr_ids=md5sum&attr_ids=genomeRunning the server in DockerBuilding imagePrimary image:docker build -t databio/bedhost -f .Dockerfile .Dev imagedocker build -t databio/bedhost:dev -f dev.Dockerfile .Test image:docker build -t databio/bedhost:dev -f test.Dockerfile .Existing images can be foundat dockerhub.Running container for developmentConfiguration settings and deployment instructions are in thebedbase.orgrepository.
Package: bedparse
BedparseBedparse is a simple python module and CLI tool to perform common operations on BED files.It offers 11 sub-commands that implement the following functionality:filter: Filtering of transcripts based on annotationsjoin: Joining of annotation files based on transcript namesgtf2bed: Conversion from GTF to BED formatconvertChr: Conversion from UCSC to Ensembl chromosome names (and viceversa)bed12tobed6: Conversion from bed12 to bed6promoter: Promoter reportingintrons: Intron reportingcds: CDS reporting3pUTRand5pUTR: UTR reportingvalidateFormat: Check that the file conforms with the BED formatInstallationInstalling is as simple as:pip install bedparseBasic usageThe basic syntax in the form:bedparse subcommand [parameters].For a list of all subcommands and a brief explanation of what they do, use:bedparse --help.For a detailed explanation of each subcommand and a list of its parameters, use the--helpoption after the subcommand's name, e.g.:bedparse promoter --helpDocumentationOur documentation is hosted onRead the Docs.We also have a shorttutorialto guide you through the basic functions.PublicationsIf you use bedparse please cite the followingpaper:Leonardi, (2019). Bedparse: feature extraction from BED files. Journal of Open Source Software, 4(34), 1228,https://doi.org/10.21105/joss.01228
Package: bed-reader
Read and write the PLINK BED format, simply and efficiently.This is the Python README. For Rust, seeREADME-rust.md.HighlightsFast multi-threaded Rust engine.Supports all Python indexing methods. Slice data by individuals (samples) and/or SNPs (variants).Used byPySnpTools,FaST-LMM, andPyStatGen.SupportsPLINK 1.9.Read data locally or from the cloud, efficiently and directly.InstallFull version: With all optional dependencies:pip install bed-reader[samples,sparse]Minimal version: Depends only onnumpy:pip install bed-readerUsageRead genomic data from a .bed file.>>>importnumpyasnp>>>frombed_readerimportopen_bed,sample_file>>>>>>file_name=sample_file("small.bed")>>>bed=open_bed(file_name)>>>val=bed.read()>>>print(val)[[1.0.nan0.][2.0.nan2.][0.1.2.0.]]>>>delbedRead every second individual and SNPs (variants) from 20 to 30.>>>file_name2=sample_file("some_missing.bed")>>>bed2=open_bed(file_name2)>>>val2=bed2.read(index=np.s_[::2,20:30])>>>print(val2.shape)(50,10)>>>delbed2List the first 5 individual (sample) ids, the
first 5 SNP (variant) ids, and every unique
chromosome. Then, read every genomic value in chromosome 5.>>>withopen_bed(file_name2)asbed3:...print(bed3.iid[:5])...print(bed3.sid[:5])...print(np.unique(bed3.chromosome))...val3=bed3.read(index=np.s_[:,bed3.chromosome=='5'])...print(val3.shape)['iid_0''iid_1''iid_2''iid_3''iid_4']['sid_0''sid_1''sid_2''sid_3''sid_4']['1''10''11''12''13''14''15''16''17''18''19''2''20''21''22''3''4''5''6''7''8''9'](100,6)From the cloud: open a file and read data for one SNP (variant)
at index position 2.>>>withopen_bed("https://raw.githubusercontent.com/fastlmm/bed-sample-files/main/small.bed")asbed:...val=bed.read(index=np.s_[:,2],dtype="float64")...print(val)[[nan][nan][2.]]Project LinksDocumentationQuestions to:fastlmm-dev@python.orgSource codePyPIBug reportsMailing listProject WebsiteChange Log
Package: bedrock
You have discovered bedrockBedrockis a high-level text pre-processing API, written in Python
and can run on NLTK or Spacy as its backends. It allows you to quickly
perform the text processing groundwork without having. It does the
menial work, so you don’t have to.Use this library if you find the following highlights useful: * Fast
prototyping * Switching between different backends * Work in batches,
rather than writing loops * Support for DataFrame inputs/outputsInstallbedrockin a jiffy:pipinstallbedrockbedrockdownloadallFrom zero to bedrock hero in 10 secondsNow you can runimportbedrockbedrock.process.pipeline('Hallo Welt')Congrats! :tada:Engines and LanguagesCurrentlybedrocksupports the following engines: * spacy * nltkAnd the following languages and corresponding download arguments: *
English (‘en’ or ‘english’) * German (‘de’, ‘german’ or ‘deutsch’)Installation and usagePackage installationpipinstallbedrockInstall support for all languages:bedrockdownloadallInstall support only for English:bedrockdownloadenInstall support for German:bedrockdownloaddeImport modules from package in your code:frombedrockimportprocess# Processing textsfrombedrockimportcollection# Loading data collectionsfrombedrockimportcommon# Some common functionsfrombedrockimportfeature# Feature extractionfrombedrockimportviz# Visualizations