Saravanan666/pypi-org huggingface dataset:
Package: exoclasma-index
exoclasma-indexDescriptionexoclasma-index is a tools for reference sequence and capture intervals preparation, a part of upcoming ExoClasma Suite.Features:Prepare FASTA reference sequence (purge names, uncompress, sort and filter contigs, etc.)Create restriction sites forJuiceras described atconfig.json.
For now available restrictases include:HindIIIDpnIIMboISau3AIArimaAdd your own restriction sites.Create indices for:SAMtools (samtools faidx)BWA (bwa index)optional: GATK (gatk CreateSequenceDictionary)Also, the tool can check and prepare exome BED files (captures).This is a pre-release. Use it at your own risk!Installationpython3-mpipinstallexoclasma-indexCommand-line dependenciesSAMtoolsBWABEDtoolsGATKFirst three are available at Ubuntu repos:aptinstallsamtoolsbwabedtoolsGATK should be installed into Miniconda environmentas described by the developer.UsageReference preparationexoclasma-indexReference-f${FastaFile}-n${ReferenceName}-p${ParentDirectory}Optional:-d ${ReferenceDescription},--no-gatk,-c ${Contigs}.Contigs may be filtered or sorted with-coption.
Full list of FASTA contigs can be displayed viaexoclasma-indexContigs-f${FastaFile}Capture preparationexoclasma-indexCapture-b${BedFile}-n${CaptureName}-g${GenomeInfoJSON}GenomeInfoJSONis a JSON file which created viaexoclasma-index Reference.Optional:-d ${ReferenceDescription}Restriction sites manipulationRestriction sites can be displayed, added, or removed:exoclasma-indexRestrictionSites
exoclasma-indexAddRS-n${RestrictionSiteName}-r''${RestrictionSiteRegExp}''exoclasma-indexRemoveRS-n${RestrictionSiteName}
Package: exoclasma-note
exoclasma-noteAnnotation of genomic variants.DependenciesPerl:sudoaptinstallperlAnnovar:GENOME="hg19"# hg38 if you prefercurl--outputannovar.latest.tar.gzwww.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar-xzfannovar.latest.tar.gzcdannovarfordatabaseinrefGeneknownGeneensGenedbnsfp35cdbscsnv11intervar_20180118gnomad211_genomegene4denovo201907kaviar_20150923hrcr1abraom1000g2015auggmeesp6500siv2_allavsnp150clinvar_20200316regsnpintronrevelgwava;do{perlannotate_variation.pl-downdb-buildver${GENOME}-webfromannovar${database}humandb/}donecd..
rmannovar.latest.tar.gzInstallsudopython3-mpipinstallexoclasma-noteUsageexoclasma-note-u${unit_json}-a${annovar_folder}-g${genome}[--nofilter]unit_json: Unit JSON file which was created by exoclasma-pipeannovar_folder: Path to ANNOVAR folder where perl scripts are locatedgenome: Genome assembly which use ANNOVAR (i.e., hg19, hg38, etc.)
Package: exoclasma-pipe
exoclasma-pipeDescriptionexoclasma-pipe is a tool for reads quality control, adapters removing, mapping, and variant calling, a part of upcoming ExoClasma Suite.Features:Pool FastQ quality control via FastQCMapping pipeline: cutadapt + BWA + GATK MarkDuplicatesVariant calling pipeline: GATK BQSR + GATK HaplotypeCallerThis is a pre-release. Use it at your own risk!Installationpython3-mpipinstallexoclasma-pipeCommand-line dependenciesSAMtoolsBWABEDtoolsFastQCcutadaptGATKFirst five are available at Ubuntu repos:aptinstallsamtoolssamtoolsbwabedtoolsfastqccutadaptGATK should be installed into Miniconda environmentas described by the developer.UsageFastQCexoclasma-pipeFastQC-f${file_1}${mask_1}${file_2}-d${output_folder}Alignexoclasma-pipeAlign-u${unit_json_file}Unit JSON describes a job for pipeline.
It must have the following format:{"ID":"Scc3-WXS","Description":"Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages (SRX11913458)","ParentDir":"testoutput","Input":[{"Files":{"R1":"testdata/test_scc3_R1.fastq.gz","R2":"testdata/test_scc3_R2.fastq.gz","Unpaired":null},"RG":{"Sample":"Scc3","Library":"LY0200-I","Platform":"ILLUMINA","Instrument":"IlluminaHiSeq2500","Lane":"1","Barcode":"ACGTAT"},"Adapter":"illumina"}],"Reference":{"GenomeInfo":"testdata/testReference/testReference.info.json","Capture":"testCapture"},"Config":{"Threads":4,"RemoveTempFiles":true}}Reference with GenomeInfo file and Captures can be prepared withexoclasma-index.Callexoclasma-pipeCall-u${unit_json_file}-d${dbSNP_vcf_gz}Here you will need a Unit JSON file which was created withexoclasma-pipe Align.
dbSNP will be used for BQSR stage.
Package: exocode
ExoCodeGenerates .csv files including data on the existence of various features of interest
from the Digitized Sky Survey (DSS), 2-micron All Sky Survey (2MASS), and
Wide-field Infrared Survey Explorer (WISE) image catalogs. The goal is to use the
data to identify candidates that might have circumstellar debris disks.This release (1.2.0) includes catalogs tycho_2mass_wise-XMATCH-POS.csv (full catalog), RandSample+1000.csv,
RandSample+2000.csv, and tam_cat_sample.csv. Pre-downloaded images from tam_cat_sample.csv are available
for your convenience in FITS/Tam/. All other catalogs must first have images downloaded to be useful.SeeCHANGES.txtfor more detailed updates with this release, or the documentation (included in package,
plus link at bottom).Dependent on scikit-image (skimage), matplotlib, numpy, and astropy.Lives athttps://bitbucket.org/leckman/exoplanets/overviewTO USE:Use dataAcq.py to retrieve the images for one of the provided catalogs in  Catalogs/You can also use one of your own, provided the format remains the same: ra,dec (degrees)Data included for tam_cat_sample.csv catalog under FITS/TAM/Use dataGen.py to run analysis on the downloaded images and output the results to a new .csvRun Guidelines:Command line: (in containing directory)cd srcpython dataGen.pyIn python:import src.dataGenNew Graphical Interfacerun applicationselect desired catalogfollow prompts to gather data, flip through indices, display imagescan be run using $ ./GUI.sh in src directoryalternatively, use $ python GUI.pyFull Documentation:https://docs.google.com/document/d/1-QtbvASw43S03IHlEPk4qlstk8aNtAmu8uT2uNk6otY/edit?usp=sharing
Package: exocolours
ProofUtils ✨📝 Information:An easy-to-use package used for generatingcoloron console. 🤖It usescoloramato return an image of your console!📥 Installation:You are able toinstallthe package directly throughpipusing the following command:pip install exocoloursThen simply import the package and use it as you wish.👨‍💻 Example:Here's a simple example of using exocolours.fromExoColoursimportexocoloursprint(exocolours.color_text("Hello, World!",exocolours.RED))📚 Formatting:FormatDescriptionPingsUse[PING]to represent a ping.New LineUse\nto represent a new line instead of creating more items in the messages list!Coming SoonWe are planning on addingcodeblocks,boldingand the rest of the Discord formats soon!ContributingAll contributions are appreciated. To contribute to the package, open apull request. 🙏
Package: exocounts
ExocountsExocounts computes various statistical noises of astronomical photon counts observations. Very easy task? Yes, I know, but people sometimes make mistakes in photon number calculations, which can have serious consequences.Exocounts defines InstClass, TargetClass, ObsClass, something like that.ejas=exocounts.InstClass()ejas.lamb=1.35*u.micron#micronejas.dlam=0.5*u.micron#micronejas.dtel=0.35*u.m#telescope diameter mejas.dstel=0.14*u.m#secondary telescope diameter m or 12.4 (3 tels)ejas.throughput=0.8ejas.ndark=15.5/u.s#dark currentejas.nread=15.0#nrejas.fullwell=150000.target=exocounts.TargetClass()target.teff=3000.0*u.K#Ktarget.rstar=0.2*const.R_sun#Rsolartarget.d=15.0*u.pc#pcobs=exocounts.ObsClass(ejas,target)obs.texposure=0.0833*u.h#cadence [hour]obs.tframe=12.5*u.s#time for one frame [sec]obs.napix=15# number of the pixels in apertureS=1.8*1.8*np.pi#core sizeobs.effnpix=S/3.0#3 is an approx. increment factor of PSFand then you can compute noises like that.print("photon/pix/frame=",obs.nphoton_frame)print("shot noise (sigma) in total [ppm]=",obs.sign_relative*1.e-6)print("dark in total  [ppm]=",obs.sigd_relative*1.e-6)print("readout in total  [ppm]=",obs.sigr_relative*1.e-6)
Package: exodar
ID GeneratorA package used to generate random ids of variable lengths and types.How to useAfter installing the package use following import:from idgenerator import generate_password,generate_guid,generate_credit_card_number,
generate_pin_number,
generate_object_idThen use following commands:password = generate_password(length= 'your_desired_length')guid = generate_guid()credit_card_number = generate_credit_card_number(length='your_desired_length')pin = generate_pin_number(length='your_desired_length')objid = generate_object_id()
Package: exodusHcat
ExodusHcatConvertor .seco file from Exodus Wallet, seco to hashcat stringInstallationPython requiresPython.orgv3,7+ to run.
Install the dependencies and devDependencies and start the server.python-mpipinstallpip
python-mpipinstall--upgradepip
pipinstallExodushcatUsingfromExodushcatimportextractHashcathashcat=extractHashcat(r"C:\Users\Administrator\Desktop\seed.seco")print(hashcat)######Output:EXODUS:16384:8:1:tKHsGN1+vypJCD8weCMAzh4TJ2gvpFQsLCz3DU3RI18=:xCH6jPc2YoSx94oM:9a3nb9oOKhp3z2pgAFE0y3HNBKkKXFnyk90oNMunEqE=:CAgoIaKpjc+nkGUu5rGdIA==LicenseMITEncode Cipherbcrypt group
Package: exodusreader
exodusReaderReader for exodus filesTodos to setup projectin gitlab activate CI/CD (settings→general→visibility→CI/CD)create token for pypi (todo: more text)adapt coverage percentageFeaturesFree software: BSD licenseDocumentationTODO: describe featuresInstallationInstallation from sourceGet exodusreader source fromhttps://gitlab.dlr.de/fa_sw/peridynamik/exodusreader.gitand add the /src folder to pythonpath in the environment variablesInstallation as python packageInstall it fromthe gitlab packacke registryYou can download the latest artifact (*.whl) and install it usingcd exodusreader
python setup.py install exodusreader.whlTest the installationIn python execute:import exodusreaderDevelopersDevelopers may also install the pre-commit hook.Precommitinstall the pre-commitpip install pre-commit
or
conda isntall pre-commitIn the exodusreader folderpre-commit installThis enables the pre-commit hooks defined in.pre-commit-config.yamland eases your commits and successful pipline runs.UsageContributing toexodusreaderWe welcome your contribution!If you want to provide a code change, please:Create a fork of the GitLab project.Develop the feature/patchProvide a merge request.If it is the first time that you contribute, please add yourself to the list
of contributors below.CitingNo citing requiredLicenseFree software: BSD licenseDocumentation:https://exodusreader.readthedocs.io.Change LogseechangelogCI Pipeline and Jobs for DevelopersIf you encounter any failed job on the pipeline you can run them locally for more information.
(prerequisite: havemakeandpoetryinstalled [e.g. conda install make poetry])See all availabe make targets used for the ci-jobsmake listFind the target with matching names and execute them locally e.g.:make testIfcheck-formattingfails, run the following to fix issues.make formattingIfcheck-license-metadatafails, runmake check-license-metadataidentify the corresponding filename and run the following (include the filename in $filename)poetry run reuse addheader --copyright="German Aerospace Center (DLR)" --license="MIT" $filenameAuthorsJan-Timo Hesse
Package: exodusutils
Exodus common utilitiesThis is the library defining the schemas for exodus utilities.StructureexodusutilsContains helpful utility functions.schemasIn theschemasfolder you can find the following:Schema definitions for the model algorithm's incoming requestsSchema definitions for the model algorithm's responsesDefinitions forRegressionScoresandClassificationScoresDefinitions for types such asAttributeandColumnpredictThepredictfolder contains helper functions for prediction.enums.pyContains enums used by Exodus. Current contains the following:TimeUnit, with helper methods to convert timestamps to different formatsDataType, with helper methods to convert fromPandastypesfeature_engineering.pyContains commonly used feature engineering methods. Currently includes:One-hot encodingLabel encodingTime component encoding
It is recommended to use at least 1 method in this file during training.frame_manipulation.pyContains multiple frame manipulation methods. Used during prediction, should pick the method that corresponds to the one used during training.frames.pyContains definitions and helper functions for the following classes:SplitFrames: A 3-tuple with a training dataframe, a testing dataframe, and a validation dataframe.CVFrames: A list ofSplitFrames. Should not be instantiated manually, user should useCVFrames.iidhelper classmethod.
Package: exoedge
ExoEdgeExoEdge is the Exosite's developed and maintained client toExoSense <https://docs.exosite.io>_. ExoSense provides configuration objects that conform to data schemas. ExoEdge interprets these schema-driven objects and configures industrial IoT gateways to give their data to ExoSense according to schema. ExoEdge is a schema based IIoT gateway that runs on most linux-based platforms.RequirementsPython 3.5+NOTE:In most cases, having a linux gateway is enough as long as the Python requirements are met. ExoEdge is pure-python, which means there is no need forgccorpython-devin order to install and run it.For information on ExoEdge usage or getting ExoSense for your solution, emailSupport <support@exosite.com>_ or visitExoSense <https://docs.exosite.io/exoedge/>_.
Package: exoedge-ethernetip
DescriptionWarning:Currently only compatible with Python3 (>=3.6.1)The purpose of this repository is to provide an ExoEdge protocol source that can get read EtherNet/IP tags from a PLC.A protocol source (often just referred to as a “source”) is the glue between ExoEdge and the field-bus that you want to get data to and from. It is helpful to think of a source as a plugin to ExoEdge.This source utilizes thepycomm3library and is subject to the same restrictions.InstallInstalling a build can be done in several ways:Installing From Source$pythonsetup.pyinstallInstalling From Builds$pipinstalldist/*.whlInstalling From Builds$pipinstallexoedge_ethernetipUsageConfigure the channel in ExoSense by inputting an Application of ‘EtherNetIP’ and including both ‘path’ and ‘tag’ in the app_specfic_configThepathargument can take 3 forms:IP Address Only (10.20.30.100) - Use if PLC is in slot 0 or if connecting to CompactLogixIP Address/Slot (10.20.30.100/1) - Use if PLC is not in slot 0CIP Routing Path (10.20.30.100/backplane/3/enet/10.20.40.100/backplane/0) - Use for more complex routing
Package: exoedge-fileio
DescriptionThe purpose of this repository is to provide an ExoEdge protocol source that uses a text files as the input and output.A protocol source (often just referred to as a “source”) is the glue between ExoEdge and the field-bus that you want to get data to and from. It is helpful to think of a source as a plugin to ExoEdge.Current UsageCurrently, the source will read from a file and push the last line of data to ExoSense.This can be used either by overwriting the file (always one line in the file) or appending the input file with a new line to keep historical information on the edge.Planned FeaturesImplement output_file for controlling the deviceAdd custom delimiterInstallInstalling a build can be done in several ways:Installing From Source$pythonsetup.pyinstallInstalling From Builds$pipinstalldist/*.whlInstalling From Builds$pipinstallexoedge_fileioExoSense ConfigurationBelow is an example config_io for reading from input_file and using output_file for device control.{"channels":{"000":{"channel_name":"000","description":"File Reader","display_name":"FileIO","properties":{"data_type":"TEMPERATURE","data_unit":"DEG_FAHRENHEIT","device_diagnostic":false,"max":null,"min":null,"precision":2},"protocol_config":{"app_specific_config":{"input_file":"<Fully qualified path to file>","output_file":"<Fully qualified path to file>"},"application":"FileIO","down_sample":"actual","input_raw":{},"interface":null,"report_on_change":false,"report_rate":10000,"sample_rate":10000,"timeout":null}}}}Example Protocol Configuration in ExoSenseDevice ControlDevice control is available by using an “output_file” in the app_specific_configExoEdge will write the Device Control (data_out) value to this file. It will also write the latest value upon starting (in case the value was set when the device was off).
Package: exoedge-linuxstats
DescriptionThe purpose of this repository is to provide an ExoEdge protocol source that can report linux system information.A protocol source (often just referred to as a “source”) is the glue between ExoEdge and the field-bus that you want to get data to and from. It is helpful to think of a source as a plugin to ExoEdge.Available FunctionstimeDisplays the current time in the format “HH:MM:SS”datetimeDisplays the current datetime of the device in the format “YYYY-MM-DD HH:MM:SS.sss”cpuDisplays the current CPU usage as a percentmemDisplays the current memory usage as a percentinterfacesRequires ‘/sbin/ifconfig’ or ‘ip a’ to execute on the device.
Displays the active interfaces and their IP addresses in a JSON format. Use the ‘JSON Table’ panel to view.InstallInstalling a build can be done in several ways:Installing From Source$pythonsetup.pyinstallInstalling From Builds$pipinstalldist/*.whlInstalling From Builds$pipinstallexoedge_linuxstats
Package: exoedge-modbus
DescriptionThis project is a Modbus source for Exosite’sExoSensewhich usesExoEdge.InstallFrom Sourcepip install -r requirements.txt
python setup.py installFrom PyPiThe wheel for this hasn’t been published yet.pip install exoedge_modbusExoEdge ConfigurationIn order to start using this Modbus source, start theedgeddaemon with your desired parameters. For more information onedged, visitExoEdgeon PyPi.Example$ cat modbus-test1.ini
[device]
murano_host = mqtt://f5330e5s8cho0000.m2.exosite.io/
murano_id = modbus-test1
$ edged -i modbus-test1.ini goExoSense ConfigurationBelow is an exampleconfig_iosettings that illustrates how Modbus RTU data can be sent to ExoSense via ExoEdge.{"channels":{"001":{"display_name":"Input Register 1","description":"Input Register 1.","channel_name":"001","properties":{"data_unit":"NUMBER","data_type":"TEMPERATURE","min":null,"max":null,"precision":null,"device_diagnostic":false},"protocol_config":{"timeout":null,"report_on_change":false,"report_rate":2000,"application":"Modbus_RTU","app_specific_config":{"byte_endianness":"big","register_range":"INPUT_REGISTER","register_offset":"0002","register_count":1,"register_endianness":"big","bitmask":"0xffffffff","slave_id":1,"evaluation_mode":"unsigned"},"sample_rate":2000,"input_raw":{},"offset":0,"interface":"/dev/ttyM0","down_sample":"ACT"}}}}Below is theconfig_applicationsconfiguration needed for theconfig_ioabove:{"applications":{"Modbus_RTU":{"application_display_name":"Modbus RTU","interfaces":[{"interface":"/dev/ttyM0","baud_rate":19200,"stop_bits":1,"data_bits":7,"parity":"none"}]}}}Below is aconfig_ioexample forModbus_TCP:{"channels":{"1":{"display_name":"Input Register 1","description":"One-second intervals of input register 1.","properties":{"max":null,"precision":null,"data_type":"BINARY","min":null},"protocol_config":{"application":"Modbus_TCP","report_on_change":false,"report_rate":1000,"sample_rate":1000,"down_sample":"ACT","app_specific_config":{"ip_address":"192.168.11.139","port":5020,"register_range":"INPUT_REGISTER","register_offset":0,"register_count":1,"byte_endianness":"big","register_endianness":"big","evaluation_mode":"string-ascii","bitmask":"0x0000"}}}}}For linux userUsers should not run exoedge withsudofor security reasons. If you getpermission denied: could not open portwhen using Modbus_RTU, try:groups${USER}This will list all the groups you belong to. If you don’t belong to the dialout group then add yourself to it, for example:sudogpasswd--add${USER}dialoutYou then need to log out and log back in again for it to be effective.
Package: exoedge-simulator
DescriptionThis project is a Simulator source for Exosite’sExoSensewhich usesExoEdgeInstallInstalling a build can be done in several ways:Installing From Source$pythonsetup.pyinstallInstalling From Builds$pipinstalldist/*.whlInstalling From Builds$pipinstallexoedge_simulatorExoSense ConfigurationBelow is an example config_io that works for generating a sin_wave{"channels":{"000":{"channel_name":"000","description":"Sin Wave","display_name":"Sin Wave","properties":{"data_type":"TEMPERATURE","data_unit":"DEG_FAHRENHEIT","device_diagnostic":false,"max":null,"min":null,"precision":2},"protocol_config":{"app_specific_config":{"function":"sin_wave","parameters":{"amplitude":1,"offset":0,"period":60,"precision":2}},"application":"Simulator","down_sample":"ACT","input_raw":{},"interface":null,"report_on_change":false,"report_rate":10000,"sample_rate":10000,"timeout":null}}}}Available FunctionsThe following are functions supported by the simulator, including their parameters with defaults.
Additional parameters can be included, and will be ignored.fourteenReturns 14"function":"fourteen","parameters":{}current_timeReturns the current timestamp"function":"current_time","parameters":{}echoEcho a value into a string"function":"echo","parameters":{"value":"Hello World"}strip_non_numericStrip out non-numeric characters from string"function":"strip_non_numeric","parameters":{"value":"1234BEEF"}sin_waveGenerate a sin wave from the current time"function":"sin_wave","parameters":{"period":60,"amplitude":1,"offset":0,"precision":2}cos_waveGenerate a cos wave from the current time"function":"cos_wave","parameters":{"period":60,"amplitude":1,"offset":0,"precision":2}locationGenerate location data from the current time and a starting locationMoves in a circle everyperiodseconds. Path isradiusdecimal degrees
from the center point defined bylatitudeandlongitude."function":"location","parameters":{"latitude":None,"longitude":None,"period":60,"radius":0.1,"precision":6}random_integerGet a random integer between two values"function":"random_integer","parameters":{"lower":0,"upper":10}random_sleepSleep for a random number of seconds"function":"random_sleep","parameters":{"lower":0,"upper":10}ip_addressReturns a string that represents the ip address in octet form of the iface parameter given.Parameters:interface: The network interface. Useifconfig(MAC, linux) oripconfig(Windows) to check the interface."function":"ip_address","parameters":{"interface":"en0"}return something like: {“000”: [“192.168.2.143”]}
Package: exofrills
You might be looking for help, but this is all I can do:usage: xo [-h] path

exofrills: your text has been edited...but you are still hungry.

positional arguments:
  path        path to file, may include colon separated line and col numbers,
              eg 'path/to/xo.py:10:42'

optional arguments:
  -h, --help  show this help message and exitSomeone else made avideo tutorialand posted
it on YouTube within an hour of the 0.1 release.get xoInstall from the cheeese shop withpiporeasy_install:$pipinstallexofrills$easy_installexofrillsFork xo fromgithub:$gitclonehttps://github.com/scopatz/xo.gitkey commandsesc:get helpctrl + o:save file (write-out)ctrl + x:exit (does not save)meta + s:select pygments stylectrl + f:insert file at current positionctrl + y:go to line & column (yalla, let’s bounce)ctrl + n:name completion with Jedi (if installed)ctrl + k:cuts the current line to the clipboardctrl + u:pastes the clipboard to the current linectrl + t:clears the clipboard (these spell K-U-T)ctrl + w:set regular expression and jump to first matchmeta + w:jump to next match of current regular expressionctrl + r:set substitution for regular expression and replace first matchmeta + r:replace next match of current regular expression