Saravanan666/pypi-org huggingface dataset:
Package: covidpy
covidpyDetailed Regular Information about World's Covid19 DataFeaturesGet Worlds Covid19 StatusGet All Country's Covid19 StatusGet Individual Countriy's Covid19 StatusRequirementspython >= 3.6InstallationInstall the dependencies and devDependencies and start the server.pip install covidpyDependenciespandas
requests
beautifulsoup4FunctionsInstructions on how to use them in your own application are linked below.FunctionsWorkWorldData()Get Worldwide DataListCountries()Get Total Country ListCountryData(country)Get Individual Country's DataAllData()Get All Country's DataUsageGet Worldwide Datafrom covidpy import WorldData

world = WorldData()
print(world)Result:{
    'Total_Cases': 161080616, 
    'New_Cases': 3853,
    'Total_Deaths': 3345018,
    'New_Deaths': 274,
    'Total_Recovered': 139849282,
    'New_Recovered': 2483,
    'Active_Cases': 17886316,
    'Serious_Cases': 105218
}Get Country Listfrom covidpy import ListCountries

countries = ListCountries()
print(countries)Result:Country_ID      Country_Name
1             1     NORTH AMERICA
2             2              ASIA
3             3     SOUTH AMERICA
4             4            EUROPE
5             5            AFRICA
..          ...               ...
225         226  MARSHALL ISLANDS
226         227             SAMOA
227         228      SAINT HELENA
228         229        MICRONESIA
229         230             CHINAGet All Countries Datafrom covidpy import AllData

all_data = AllData()
print(all_data)Result:[
    {
        'Country_Name': 'USA', 
        'Total_Cases': 33586136, 
        'New_Cases': 0, 
        'Total_Deaths': 597785, 
        'New_Deaths': 0, 
        'Total_Recovered': 26620229, 
        'New_Recovered': 0, 
        'Active_Cases': 6368122, 
        'Serious_Cases': 8707, 
        'Total_Tests': 461476543
    },
    {
        'Country_Name': 'INDIA', 
        'Total_Cases': 23702832, 
        'New_Cases': 0, 
        'Total_Deaths': 258351, 
        'New_Deaths': 0, 
        'Total_Recovered': 19728436, 
        'New_Recovered': 0, 
        'Active_Cases': 3716045, 
        'Serious_Cases': 8944, 
        'Total_Tests': 307583991
    },
    ...
]Get Individual Country Datafrom covidpy import CountryData

country = CountryData("Bangladesh")
print(country)Result:{
    'Country_Name': 'BANGLADESH', 
    'Total_Cases': 777397, 
    'New_Cases': 0, 
    'Total_Deaths': 12045, 
    'New_Deaths': 0, 
    'Total_Recovered': 718249, 
    'New_Recovered': 0, 
    'Active_Cases': 47103, 
    'Serious_Cases': 1120, 
    'Total_Tests': 5677222
}LicenseMIT
Package: covid-ru
Getting latest covid-19 stats in Russia to your cli fromстопкоронавирус.рфSynopsiscovid-ru[--all|--dead|--tests|--cases|--recovered]Installationpip installcovid-ruDescriptioncovid-ru is a small command-line tool that gets latest covid-19 in Russia stats.BugsBugs should be reportedhere.
Package: covidsafescan
covidsafescanUses Bluetooth to scan to covidsafe apps.Install withpip3 install covidsafescanusage: covidsafescan [-h] [--debug] [--json] [--timeout TIMEOUT] [--once]
                     [--no-adv-uuids] [--no-adv-manuf] [--apple] [--passive]

Covidsafe BLE Scanner

optional arguments:
  -h, --help         show this help message and exit
  --debug            Enables logs
  --json             JSON Output
  --timeout TIMEOUT  Timeout, in seconds (default: 15)
  --once             Only run once
  --no-adv-uuids     Don't use UUIDs in advertisement frames to find CovidSafe
  --no-adv-manuf     Don't use Withings Manufacturer Data in advertisement
                     frames to find CovidSafe
  --apple            Use Apple Overflow Area to find CovidSafe (experimental,
                     may crash!)
  --passive          Don't try to exchange GATT details, just report MAC
                     addresses
Package: covid-seird
covid-seirdAboutcovid-seirdis a small Python package inspired by Henri Froese's post'Infectious Disease Modelling: Beyond the Basic SIR Model'.It implements theSEIRD Epidemiological Modelon COVID-19 data.First, itfitsa the SEIRD Model into the real timeline data of confirmed cases of COVID-19 of a country.Then, itsimulatesthe SEIRD curves based on the previously fitted Model.As a result, the country'sbasic reproduction number (Ro)of COVID-19 is computed.Also, thefit and simulation plotsare available.NOTE:
The COVID-19 timelines data are obtained using theCOVID19Py packagein order to retrieve the Worldwide Data repository operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE).InstallationIn order to install this package, simply run:pipinstallcovid-seirdUsageTo use covid-seird, you first need to import the package and then create a new instance, passing the country code as a parameter:fromcovid_seirdimportCountryCovidSeirdbrazil=CountryCovidSeird("br")Getting the country codesCountryCovidSeird.code_search("brazil")output:{'BR':'Brazil'}Fit the SEIRD Modelbrazil.fit()After the fit method's call, the fit score (R2) can be accessed:brazil.r2output:0.797994368607109Also after fit method's call, the basic reproduction number (Ro) will be available:brazil.r0output:2.280428864655168Fit plotbrazil.plot_fit("brazil_fit_plot")a plot file named 'brazil_fit_plot' will be created.SEIRD simulationThe simulation method receives as a parameter how many days ahead of the real data the SEIRD model will be computed.brazil.simulation(days_ahead=150)The SEIRD curves can be accessed after the simulation method's callbrazil.curves['infected']output:array([4.77396851e-09,5.32992037e-09,5.95375686e-09,6.59631344e-09,7.32558927e-09,8.14396099e-09,9.05142859e-09,1.00479921e-08,...7.48473200e-03,7.06776956e-03,6.67386382e-03,6.30175876e-03,5.95026480e-03,5.61825534e-03,5.30466353e-03,5.00847963e-03])Simulation plotsbrazil.plot_simulation("brazil_simulation_plot")a plot file named 'brazil_simulation_plot' will be created.
Package: covid-spike-classification
Detect interesting SARS-CoV-2 spike protein mutations from Sanger sequencing datacovid-spike-classificationis a script to call interesting SARS-CoV-2 spike protein mutations
from Sanger sequencing to support the Danish COVID-19 monitoring efforts.Using Sanger-sequenced RT-PCR product of the spike protein, this tool should pick up all relevant
mutations currently tracked (seecovid_spike_classification/core.pyfor the full list of tracked mutations) and give a table with one row per sample and a
yes/no/failed column per tracked mutation.This workflow is built and maintained athttps://github.com/kblin/covid-spike-classificationIf you found this tool useful, please citehttps://www.medrxiv.org/content/10.1101/2021.03.27.21252266v1Installationcovid-spike-classificationis distributed via this git repository, pypi or bioconda.BiocondaInstalling via bioconda is the fastest way to get up and running:condacreate-ncsc-cconda-forge-cbiocondacovid-spike-classification
condaactivatecscgit & pypiWhen installing via git or pypi, you first need to install the external binary dependencies.covid-spike-classificationdepends on three excellent tools to do most of the work:tracy (versions 0.5.3 & 0.5.7 tested)bowtie2 (version 2.4.2 tested)samtools (versions 1.10 & 1.11 tested)If you havecondainstalled, the easiest way to get started is to just install these via callinggitclonehttps://github.com/kblin/covid-spike-classification.gitcdcovid-spike-classification
condaenvcreate-ncsc-fenvironment.yml
condaactivatecsc
pipinstall.Docker, Podman, SingularityWhile not technically an installation method,covid-spike-classificationis also shipped as an OCI container.
To use it, you ideally run the container from a workflow management system likeSnakemakeorNextflowthat will take care of mounting filesystems into the container for you.The OCI container image is available from the Docker Hubkblin/covid-spike-classificationrepository.SetupYou also need to generate the samtools and bowtie2 indices for your reference genome. We ship a
copy of NC_045512 and a script to generate these indices:condaactivatecsccdref
./build_indices.shcd..UsageAssuming you used above instructions to install via conda, you can run the tool like this:condaactivatecsc
covid-spike-classification--reference/path/to/your/reference.fasta--outdir/path/to/result/dir/path/to/sanger/reads/dir_or.zipNotably, you can provide the input either as a ZIP file or as a directory, as long as they directly contain the ab1 files you want
to run the analysis on.See also the--helpoutput for more detailed usage information.LicenseAll code is available under the Apache License version 2, see theLICENSEfile for details.
Package: covidstatetracker
COVID State TrackerCOVID State Tracker is used to interface with Pandas to more easily access COVID data published by the New York TimesInstallationUsehttps://pypi.org/project/covidstatetrackerpipinstallcovidstatetrackerRequirementsInstall pandashttps://pypi.org/project/pandas/ORpipinstallpandasInstall MatPlotLibhttps://pypi.org/project/matplotlib/orpipinstallmatplotlibUsagefromcovidstatesimportstatesstates.getDF()# returns entire us-states dataframe from NYTimes with five columns (exlcuding index): date, state, fips (ignore), cases, deathsstates.getLength()# returns number of rows in data framestates.getDate(index)# returns the date for the given index of a COVID-19 data entrystates.getState(index)# returns the name of the state for the given index of a COVID-19 data entrystates.getDeathsToDate(index)# returns total number of deaths in a certain state up to the given index of a COVID-19 data entrystates.getDailyDeathCount(index)# returns the number of deaths in a certain state that happen in a single day for a given COVID-19 data entrystates.getCasesToDate(index)# returns total number of cases in a certain state up to the given index of a COVID-19 data entrystates.getDailyCaseCount(index)# returns the number of cases in a certain state that happen in a single day for a given COVID-19 data entrystates.getDateIndex(date)# returns all the indexes of a given date in the dataframe in a liststates.getStateIndex(state)# returns all the indexes of a given state in the dataframe in a liststates.graphDateCases(state,dates)# creates line graph of dates on the x axis and cases on the y axis for a given statestates.graphDateDeaths(state,dates)# creates line graph of dates on the x axis and daily deaths on the y axis for a given statestates.getDateRange(startDate,endDate)# returns list of dates (inclusive) from start date to end startDateContributingPull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.Please make sure to update tests as appropriate.LicenseMIT LicenseCopyright (c) 2021 Devon Schwartz and Neil AylorPermission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Package: covid-stats
Covid-StatsThis package is a way to get Covid-19 statistics using worldometers. It scraps worldometers to get these. Sync-wrapper.UsageGlobal Statsimportcovidstatsprint(covidstats.Coronavirus().get_stats())Returns:Type: Dict{'cases': '243,876,219', 'deaths': '4,956,039', 'recovered': '220,976,280'}Country Statsimportcovidstatsprint(covidstats.Coronavirus().get_stats("India"))Returns:Type: List[{'Country': 'India', 'TotalCases': '34,159,562', 'NewCases': '+790', 'TotalDeaths': '453,742 ', 'NewDeaths': '', 'TotalRecovered': '33,532,126', 'ActiveCases': '+7,676', 'CriticalCases': '173,694'}]All-Country Statsimportcovidstatsprint(covidstats.Coronavirus().get_stats("ALL"))Returns:Type: ListTOO LONG TO BE SHOWN!
Package: covid-surge
Covid-surgeCOVID-19 mortality surge period calculation for communities afflicted by the corona virus SARS-CoV-2.University of Massachusetts LowellDept. of Chemical Engineering(Nuclear Program)Prof. Valmor F. de Almeida(valmor_dealmeida@uml.edu)Preprint:How Long is the Worst Part of the COVID-19 Mortality Surge?----------------------------------------------------|WORLD|---------------------------------------------------------Data source.Distribution of mortality critical surge periods for the countries with fully evolved epidemics. The average critical surge period is the number of days between the points of maximum and minimum curvatures on the sigmoid curve approximating the data. Countries to the right are less stressed than countries to the left. The colored bar plot shows locations grouped by 2-day bin widths.The world average critical surge period at the date indicated by the plot is23 days with a 3-day standard deviation.To update this plot with live data,run this Jupyter Notebook.---------------------------------------------------------|US|-------------------------------------------------------Data source.Distribution of mortality critical surge periods for the US states with fully evolved epidemics. The average critical surge period is the number of days between the points of maximum and minimum curvatures on the sigmoid curve approximating the data. Countries to the right are less stressed than countries to the left. The colored bar plot shows locations grouped by 2-day bin widths.The US state average critical surge period at the date indicated by the plot is25 days with a 3-day standard deviation.To update this plot with live data,run this Jupyter Notebook.--------------------------------------------|US State Counties/Towns (Top 3)|---------------------------------------Data source.Distribution of mortality critical surge periods for the US state New York with fully evolved epidemics. The average critical surge period is the number of days between the points of maximum and minimum curvatures on the sigmoid curve approximating the data. Countries to the right are less stressed than countries to the left. The colored bar plot shows locations grouped by 2-day bin widths.The average critical surge period at the date indicated by the plot is21 days with a 3-day standard deviation.To update this plot with live data,run this Jupyter Notebook.-------------------------------------------------------------------------------------------------------------------------Data source.-------------------------------------------------------------------------------------------------------------------------Data source.
Package: covidtracker
covidtrackerProvides basic data cleaning, wrangling and plotting of Covid tracking data in Canada.FunctionsThe covidtracker package is designed for the easy retrieval and analysis of data pertaining to Covid trends in Canada, including information about cases, vaccinations and testing. The package serves as a wrapper for the opencovid.caAPI, and provides additional helper functions for visualising the data, either as a time series or in the form of a map.get_covid_data()Retrieve cleaned and formatted data of specified type and within (optionally) provided time ranges and locationsplot_time_series()Function for plotting time series trends in Covid datacalculate_stat_summary()Function for returning key statistical information about Covid data, such as long run trends and comparisons between provincesplot_geographical()Function for plotting chloropleth maps with Covid dataSimilar PackagesThere are currently no other Python packages available that can perform the same set of data retrieval and analysis functionalities as covidtracker. There are several packages that have similar functionality, but are most are tailored either towards covid data retrieval or data visualization. The packages designed for covid data retrieval also do not use the same data source as covidtracker. Some examples of related Python packages useful for Covid data retrieval and data visualizations include:covid19dh- For Covid data retrievalcovid- For Covid data retrievalfolium- For data visualizationsplotly- For data visualizationsInstallationPlease note that due to GDAL dependencies, the package can only be directly installed on Mac OS and Linux machines. With Windows machine, becausepip install Fionadoes not work, you need to install Fiona package first, and then install our covidtracker package.Mac OS and Linux machine:$pipinstallcovidtrackerWindows machine:$condainstallFiona
$pipinstallcovidtrackerUsagefromcovidtracker.get_covid_dataimportget_covid_datafromcovidtracker.plot_geographicalimportplot_geographicalfromcovidtracker.plot_time_seriesimportplot_tsfromcovidtracker.calculate_stat_summaryimportcalculate_stat_summarycovid_df=get_covid_data('active')head(covid_df)covid_df=get_covid_data()plot_geographical(covid_df,'cases')plot_ts(covid_df,"cases")summary=calculate_stat_summary(covid_df,'cases')DocumentationDetailed documentation for the package can be found here on Read the Docs :https://covidtracker.readthedocs.io/en/latest/ContributingWe welcome and recognize all contributions. Please see contributing guidelines in the Contributing document. This repository is currently maintained byCuthbert Chow (@cuthchow)Tianwei Wang (@Davidwang11)Siqi Tao (@SiqiTao)Jessie Wong (@jessie14)Licensecovidtrackerwas created by Group 28. It is licensed under the terms of the MIT license.Creditscovidtrackerwas created withcookiecutterand thepy-pkgs-cookiecuttertemplate.
Package: covidtracking
Covid Tracking APISimple API to get data fromhttps://covidtracking.com>>>importsys>>>sys.path.append('src')>>>fromcovidtrackingimportCovidTracking>>>c=CovidTracking()>>>x=c.states()# Get all states>>>ga=c.states('GA')# Get only Georgia data>>>twoStates=c.states('GA','SC')# You can pass multiple filtersThe data is cached, since it's not updated constantly. To refresh, callclear()first.
Package: covid-tracking-project
covid-tracking-projectA python wrapper for the Covid Tracking Project API.Installationpip3 install covid-tracking-projectImportingimport ctpFunctionsClass:us()Function:history()Description: Get US historical dataParameters:day (description: Get data on a specific day, type: string/int, requirement: optional, defaults: all days, example:20200501)Function:current()Description: Get current US dataClass:states()Function:metadata()Description: Get state metadataParameters:state (description: Get data on a specific state, type: string, requirement: optional, default: all states, example:ca)Function:history()Description: Get state historical dataParameters:day (description: Get data on a specific day, type: string/int, requirement: optional, defaults: all days, example:20200501)state (description: Get data on a specific state, type: string, requirement: optional, default: all states, example:ca)Function:current()Description: Get state current dataParameters:state (description: Get data on a specific state, type: string, requirement: optional, default: all states, example:ca)
Package: covid-util
covid-utilCLI tool for uploading and downloading files from the EMBL-EBI hosted Embassy cloud infrastructurePyPi:https://pypi.org/project/covid-util/UsersPrerequisitesUsers need to haveBasic command-line knowledgePython3.x installed on their machineCredentials to access data in the S3 bucket (access and secret keys)InstallGetcovid-utilfrom PyPi.$pipinstallcovid-utilUsageDisplay help$covid-util-h
usage:covid-util[-h][--profilePROFILE]{config,create,select,dir,clear,list,upload,download,delete}In the above, optional arguments are between[]and choices between{}.The basic usage is as follows:$covid-utilcmdARG1ARG2-o1-o2Use the tool by specifying a command (cmd- see list below) to run, any mandatory (positional) arguments (e.g.ARG1andARG2- see positional args for each command), and any optional arguments (e.g.-o1ando2- see options for each command).List of commandshelp for a specific command:$covid-util<command>-hSome commands or options/flags are restricted to authorised users (for e.g. wranglers, admin) only.configcommandConfigure AWS credentials$covid-utilconfigACCESS_KEYSECRET_KEY

positionalarguments:ACCESS_KEYAWSAccessKeyIDSECRET_KEYAWSSecretAccessKeyBy default, this tool looks for and uses the profile name _covid-util_embassy, if it exists, or it can be set by theconfigcommand.Running a command with the--profileargument uses the specified profile instead of the defaultcovid-utilprofile.createcommandCreate an upload area(authorised users only)$covid-utilcreateNAME[-p{u,ud,ux,udx}]positionalarguments:NAMEnameforthenewarea

optionalarguments:-nnameoptionalprojectnamefornewarea-p{u,ud,ux,udx}allowedactions(permissions)onnewarea.uforupload,xfordeleteanddfordownload.DefaultisuxselectcommandSelect or show the active upload area$covid-utilselectAREA

positionalarguments:AREAareauuid.IfnotpresentthenselectedareaisshownlistcommandList contents of selected area$covid-utillist[-b]optionalarguments:-blistallareasinbucket**(authorisedusersonly)**uploadcommandUpload files to the selected area$covid-utilupload(-a|-ffile[file...])[-o]optionalarguments:-auploadallfilesfromcurrentuserdirectory-ffile[file...]uploadspecifiedfile(s)-ooverwritefileswithsamenamesdownloadcommandDownload files from the selected area$covid-utildownload(-a|-ffile[file...])optionalarguments:-adownloadallfilesfromselectedarea-ffile[file...]downloadspecifiedfile(s)onlydeletecommandDelete files from the selected area$covid-utildelete(-a|-ffile[file...]|-d)optionalarguments:-adeleteallfilesfromselectedarea-ffile[file...]deletespecifiedfile(s)only-ddeleteareaandcontents**(authorisedusersonly)**
Package: covid-vaccine-stat
코로나 백신 예방 접종 통계 APIWrapper공공데이터 포털 (data.go.kr) 에서 제공하는 코로나19 예방접종 실적 통계 데이터 조회 서비스 API WrapperUsageInstall modulepipinstallcovid-vaccine-statorpipinstallgit+https://github.com/zeroday0619/covid_vaccine_stat.gitExampleSynchronousimportjsonfromcovid_vaccine_statimportsync_requestapi_key="# data.go.kr 에서 발급 받은 API Key #"res=sync_request.fetch(api_key=api_key)json_data=json.dumps(res.data[0].json(),ensure_ascii=False,escape_forward_slashes=False)print(json_data)Asynchronousimportjsonimportasynciofromcovid_vaccine_statimportasync_requestapi_key="# data.go.kr 에서 발급 받은 API Key #"loop=asyncio.get_event_loop()res=loop.run_until_complete(async_request.fetch(api_key=api_key))json_data=json.dumps(res.data[0].json(),ensure_ascii=False,escape_forward_slashes=False)print(json_data)LicenseCopyright (c) 2021 Euiseo Chazeroday0619@kakao.comDistributed under theMIT License
Package: covid-vir-assistant
A small example about virtual assistant like Siri/ Google assistant. By using wolframalpha and wikipedia as references so that please visit  wolframalpha and create application to using it. Be focus on how to use speech_recognition and UI text-to-spech, I hope you can familar with python syntax and love python more.
How to use it?Please  run pip install covid-vir-assistantRun fileinit.py / covid_vir_assistant.pyLeave anything what you need help
ex: I want to search 'Thomas Edison'. So you can type 'Thomas Edison' on this box or Press enter and say 'Thomas Edison'.Please wait and see what covid virtual assistant can do for you.Visit my github and do not hesitate to leave me comment via email.