Saravanan666/pypi-org huggingface dataset:
Package: giraffe
### Sequence Feature Detection and MappingThis repository consists of two tools: Giraffe and Hippo. Giraffe includes aset of javascripts that visualize sequences and sequence features, and a Djangoapp that detects features, restriction sites, and ORFs from a sequence. You canuse the javascripts independently from the Django program. Hippo is a Djangofrontend for managing NCBI blast databases. User can create sequences, assignthem to databases, and use Django management commands to build NCBI blastdatabases. Giraffe uses NCBI blast databases, for example, to detect featuresin a sequence.Hippo and Giraffe provide a convenient way to use Blast for your ownapplication. You can build blast databases using Hippo, then use Giraffe toblast query sequence against the database. Hippo offers a Django admin UI tomanage the blast DB, while Giraffe handles calling blast, parsing blastresults, and visualizing detected features.This software was originally written by Misha Wolfson and Benjie Chen,copyrighted by Addgene, and released under the MIT License. See LICENSE file.It is now maintained by Benjie Chen.### Giraffe - VisualizationYou can use Giraffe javascripts independently of the Django service, tovisualize a sequence you already have a list of features for.See src/giraffe/templates/giraffe/{analyze,draw}.html.### Giraffe - Sequence feature detectionRequirements:* System requirements: see provison/provision.sh (you can use this toprovision a Vagrant instance, e.g.)* Python requirements: pip install -r requirements.txt(Currently supports Django 1.5 or higher)* NCBI: install NCBI Blast toolkit (this takes awhile): cd ncbi; . installInstall Django service and build default database:```git clone git@github.com:benjiec/giraffe.gitcd giraffe(cd src; python manage.py migrate)(cd src; python manage.py build_blastdb)```Run test server:```cd src; python manage.py runserver 0.0.0.0:8000```Then goto http://0.0.0.0:8000/giraffe/demo/### APIYou can POST a sequence to "/giraffe/analyze/", with the following params:```db=default&sequence=your_dna_sequence_or_genbank_sequence_here```This will return a JSON array of [sequence_len, array of features, sequence].Programmatically, you can construct new blast databases using Hippo. E.g.```from hippo.models import Feature, Feature_Type, Feature_Databasedb = Feature_Database(name='my_db')db.save()ft = Feature_Type.objects.get(type='Promoter')feature = Feature(type=ft, name='Promoter1', sequence='AGCTATTTCGGAGTCGGCGATTACGATCGGCGATCG')feature.save()db.features.add(feature)db.build()```You can then query against database. E.g.```from hippo.models import Feature_Databasefrom giraffe.features import blastdb = Feature_Database.objects.get(name='my_db')query = '...' # some query sequencefeatures = blast(query, db)```### Hippo as a BLAST frontendUse Django admin to add features, group features into databases. Use thebuild_blastdb django management command to build your databases, then Giraffecan use the databases for feature detection. Alternatively, call the```build``` method on a ```Feature_Database object``` directly.
Package: giraffez
Giraffez is a client library forTeradata, made to be fast and user-friendly. It shares many features with the official Teradata tools, but makes them available in an easy-to-use command-line interface and Python API.FeaturesCommand-line toolPython API- expressive, powerful, and great forworking with other packages(e.g.pandas)ExecuteSQL statements using the Teradata CLIv2 library – performing ad hoc queries and commandsInsertinto existing Teradata tables using the CLIv2 driversArchiveTeradata tables to save space. These can easily betransformed to flatfilesorloadedback into TeradataBulkExportfrom Teradata to a flatfile or archival format, retaining data type informationBulkLoadinto existing Teradata tables using the Teradata PT Update (MLOAD)Config- manage connection information and credentials securely using thegiraffez configandgiraffez secretcommandsInteractive shellfor executing Teradata queries – much like BTEQ, but with a friendly interfaceRunjob files in YAML formatLinksDocumentationQuick Install$ pip install giraffezSee thesetup instructionsfor requirements and details on how to configure your environment.ContributorsWe welcome Your interest in Capital One’s Open Source Projects (the
“Project”). Any Contributor to the Project must accept and sign an
Agreement indicating agreement to the license terms below. Except for
the license granted in this Agreement to Capital One and to recipients
of software distributed by Capital One, You reserve all right, title,
and interest in and to Your Contributions; this Agreement does not
impact Your rights to use Your own Contributions for any other purposeSign the AgreementCode of ConductThis project adheres to theOpen Code of ConductBy participating, you are
expected to honor this code.Teradata is a registered trademark of Teradata Corporation
Package: girafr
GiRAFR (Guide RNA Anomalies and Functionality Revealed)GiRAFR is a python package developed to perform quality control of single cell CRISPR screens, and to assign gRNAs to cells in a sensitive, mutation-aware manner.Introduction/AbstractNovel single cell RNA-seq analysis combined with CRISPR screens enables the high- throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes are however lacking. Here, we generated a CRISPR droplet sequencing dataset. We demonstrate that the current default tool fails to detect mutant gRNAs. We therefore developed GiRAFR, a pysam-based software tool to characterize intact and mutant gRNAs. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 34 % of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens.Installationpip install girafrDocumentationSingle cell CRISPR screen gRNA library mutation profilingDetect CRISPR-Cas9 editing effects in Single cell RNA-seqOutput files formatCitationGiRAFR improves gRNA detection and annotation in single cell CRISPR screensQian Yu, Paulien Van Minsel, Eva Galle, Bernard ThienpontbioRxiv 2022.10.24.513352; doi:https://doi.org/10.1101/2022.10.24.513352License and copyright
Package: giraumon
GiraumonGiraumon is an anagram for MiroungaTools for Mirounga HostingInstallationpipinstallgiraumonorgitclonehttps://github.com/mgasystem/giraumoncdgiraumonpythonsetup.pyinstallOr in developper mode (Use virtualenv)gitclonehttps://github.com/mgasystem/giraumoncdgiraumonpythonsetup.pydevelopConfigurationNothing to configure yetUtilisationIn your repository application, use this command to initialize the files for deploymentgiraumoninit.If no git found, you can creat one with -f,–force argumentgiraumoninit--force.Changelog0.0.1 (2017-07-15)Add init subcommand to create the initial structure of folder
Package: girc
A modern Python IRC library for Python 3.4, based on asyncio. Currently in alpha.If you use this, anything can change without notice, everything can be overhauled, and development may even stop entirely without any warning.If you would like to help build this, awesome! Otherwise, I’d stay away for now and use another library:irc,irc3.Hosted DocumentationFeaturesThis library is in development, so these features may be in various levels of completion right now.Incoming and outgoing events.Info and state tracking.Server-based IRC mapping for dicts, lists, and strings.IRCv3 capability support.Escaping and unescaping IRC formatting for ease-of-use (bold, colours, etc).Why?I’ve been using another IRC library for a long time. It’s been pretty good, but I need more features. Handling both incoming and outgoing messages, automatic information tracking, converting IRC formatting (bold/colours/etc) to and from an escaped, human-readable and writable format.I’ve looked at some other libraries, but they’re usually either too low-level, too involved, or too ‘magic’ for my liking. That said, this one is planning to be pretty magic, but it’s going to be magic in a way I think makes sense.So I decided to write my own. As part ofmammon-ircd, a nice low-level library calledircreactorwas developed. This is also a chance to give that a spin from the client side, rather than the server side.Running TestsTo run the test cases, go to thetestsdirectory and run:python3-munittest, or use the./runtestsshell script (which also produces coverage graphs).AcknowledgementsWe bundle theircreactorlibrary developed as a part ofmammon-ircd. This license for this library can be found in the LICENSE.ircreactor file.
Package: girder
Data Management PlatformGirder is a free and open source web-based data management platform developed byKitwareas part of theResonantdata and analytics ecosystem.Documentation of the Girder platform can be found athttps://girder.readthedocs.io.For questions, comments, or to get in touch with the maintainers, head to ourDiscourse forum.We’d love for you tocontribute to Girder.
Package: girder-archive-access
Access files within zip and tar archives.FeaturesThis provides access to the contents of files in Girder that are in zip, tar, tar.gz, tgz, or tar.bz2 formats.  It adds a GET file/:id/archive endpoint to list the contents of such an archive and GET file/:id/archive/download to download a component of the archive.This extends the DICOM viewer plugin so that DICOMs that are stored in an archive are directly viewable in the web client.
Package: girder-client-mount
Mount a Girder server as a local FUSE mount.InstallationYou must have Python >= 3.6 and libfuse installed.Use pippip install girder-client-mountExample UsageCreate a mount directory (e.g.,mkdir /mnt/remote_girder), then mount it viagirder-client-mount /mnt/remote_girder --username= --password= --apiurl=https://data.kitware.com/api/v1You can optionally use diskcache to persist data locally.  Add appropriate options (see help for more details)girder-client-mount /mnt/remote_girder --username= --password= --apiurl=https://data.kitware.com/api/v1 --options diskcacheOn Windows, specify an available drive letter for the mount.  You probably will need to also set an environment variable to point to a libfuse compatible dll.set FUSE_LIBRARY_PATH=c:\Program Files\Dokan\DokanLibrary-1.5.0\dokanfuse1.dll
girder-client-mount A --username= --password= --apiurl=https://data.kitware.com/api/v1
Package: girder-cli-oauth-client
girder-cli-oauth-clientA Python library for performing OAuth login to a Girder 4 (Django) server.DescriptionThis provides support for authenticating with Girder 4 servers,
using the OAuth2.0 Authorization Code Grant with PKCE flow and out-of-band redirection.UsageInstall the library:pipinstallgirder-cli-oauth-clientInstantiate anOauthClientwith your application-specific configuration:fromgirder_cli_oauth_clientimportGirderCliOAuthClientoauth_client=GirderCliOAuthClient('http://localhost:8000/oauth/','1ohsuyWIx9fEsJhmAH2AWGNUqd8Wsd7LHyongtVy',['identity'],)Callloginwhen it's time to start a login flow:oauth_client.login()# open the browser to login and wait for a codeAt the start ofeveryapplication start, unconditionally callmaybe_restore_login, to attempt to
restore a login state; this will no-op if no login is present.oauth_client.maybe_restore_login()Include these headers with every API request:requests.get('http://localhost:8000/api/users/me',headers=oauth_client.auth_headers)Calllogoutto clear any active login:oauth_client.logout()Example appThis repository comes bundled with anexample application. Run it with:gitclonehttps://github.com/girder/girder-cli-oauth-client.git
pipinstall-e'.[dev]'cdexample
pythoncli.pylogin
pythoncli.pyme
Package: girder-ess-dive
girder-ess-divePlugin implementing ESS-DIVE assetstore in GirderInstallThrough PyPI:pip install girder-ess-diveLocally:git clone https://github.com/girder/girder-ess-dive.git
cd girder-ess-dive
pip install .UsageUse Swagger API to use the pluginCreate a new ESSDIVE AssetstorePOST /essdive_assetstores

Params:
name - Name of the Assetstore
url - The base URL for the ESS-DIVEImport existing data into an assetstore.Before you do this you will need to do the following in the Girder Web UI:Set the current Girder Assetstore to ESS-DIVE AssetstoreCreate a CollectionCreate a folder to import a dataset intoPOST /assetstore/{id}/import

Params
id - The Assetstore ID of the ESS-DIVE Assetstore
importPath - the ESS-DIVE dataset ID to import
destinationId - ID of a folder, collection, or user in Girder under which the data will be imported.
destinationType	- Type of the destination resource (Must be set to "Folder).Downloading dataBrowse to your collection. Data should appear there and can be clicked on to download
Package: girder-geobrowser
Girder GeoBrowserRequirementsThe GirderGeospatialPluginPlugin Installationpip install girder-geobrowserCustom Python Commandssetup.pyincludes 2 custom commands:build_ui: This command builds the frontend from theguifolder, and places the build intogeobrowser_plugin/external_web_client.clean_build: This command cleans the project of the files generated by the previous command.WARNINGThe standalone frontend will be served at/geobrowserif the built front-end path exists (i.e.python setup.py build_uihas been run), or if the mode is notdevelopment. So, if runninggirder serveindevelopmentmode, you should see no errors if the frontend is not built. However, if runninggirder serveinproductionmode, it will attempt to serve the files, regardless of if they've been built or not, throwing an error through cherrypy if they don't exist.Custom Girder CLI CommandsThis plugin adds custom Girder CLI commands:extract-geospatialThis command manually runs theGeospatialplugin on any Girder paths specified (defaults to '/'). To specify one or more path, use the-pargument. For example, to run this command on the collectionscollection1andcollection2, you would run:girder extract-geospatial -p collection/collection1 -p collection/collection2populate-collection-metaThis command populates the specified collection(s) with the provided metadata. The provided metadata must be in JSON format. The rules for setting metadata follow that of thesetMetadatafunction. This script requires that you specify 1 metadata JSON file and one or more collection IDs. For example, to populate the meta field of collections5d3201b4dbdd758d55819007and5d3201c54731b3d3a1350823, with the filemetadata.json, you would run:girder populate-collection-meta -i 5d3201b4dbdd758d55819007 -i 5d3201c54731b3d3a1350823 -d metadata.jsonTo use a Girder path instead of a collection ID, use the -p/--path option (also works with multiple):girder populate-collection-meta -p /collection/foo -d metadata.jsonWhen using this option, if the specified path doesn't exist, it will be created.Standalone Frontend SetupInstall Yarnnpm install -g yarnInstall Frontend packagescd gui
yarn installCompiles and hot-reloads for developmentyarn run serveCompiles and minifies for productionyarn run buildRun your testsyarn run testLints and fixes filesyarn run lintCustomize configurationSeeConfiguration Reference.
Package: girder-geo-heatmap
A Girder plugin showing a heatmap of geospatial items.FeaturesAt every level of the hierarchy widget, and at the list of collections and list of users, a heatmap is shown of available geospatial items.  The heatmap uses one point per geospatial item, using the centroid of the bounds reported in the geometa record.  The heatmap is fetched based on all items that the user has permissions to read.
Package: girder-geospatial
girder_geospatialInstallationInstall girder.Installgdalversion 2 or higher on to your system.To install with a wheel, run:pip install gdal -f https://manthey.github.io/large_image_wheels/If not installing with a wheel:Install gdal to your system with the instructions aboveCheck system gdal version by runninggdal-config --versionPip install the corresponding version of gdalTest your gdal installation by runningpython-c"from osgeo import gdal"Install the geospatial plugin and desired types packages.pipinstallgirder-geospatial
pipinstallgirder-geospatial-raster\girder-geospatial-vector\girder-geospatial-gridEnable Girder cache by adding following to yourgirder config file:[cache]enabled=True
cache.global.backend="dogpile.cache.memory"cache.request.backend="cherrypy_request"UsageUploading a geospatial fileAfter the plugin is enabled in Girder, simply upload a geospatial file that gdal or ogr can handle.
To see lists of supported formats see thegdalandogrformat documentation.
This plugin responds to theupload fileevent.  File uploads will trigger a handler setting geospatial metadata on the uploaded file's item automatically.Creating geospatial metadata on an already existing itemIf you already have data in Girder, and you don't want to reupload your data. There is an
endpoint which takes an item id and creates geospatial metadata on the item.curl'{girderApiUrl}/item/{itemId}/geometa'-XPUTThis endpoint will inspect the file and attach 'geometa' key to the given item.Creating arbitrary geospatial metadata on an existing itemSome users might want more control on what they are saving. The same endpoint in option 2 can be used
to create arbitrary metadata following thebase schema.
In other words, as long as you have the required parameters that are defined in the base
schema, you are free to add your own additional data for your own purposes.curl'{girderApiUrl}/item/{itemId}/geometa?geometa={geospatialMetadata}'-XPUTQuerying mongo for geospatial datasetsTo query mongo, use the following endpoint with required query parameters.curl'{girderApiUrl}/item/geometa?{necessaryQueryStringParameters}-XGETThis endpoint accepts a number of geospatial queries, including:WKT geometry and relationBounding box and relationGeojson geometry and relationLatitude, longitude and radius.When providing latitude, longitude, and radius, the relation will be always "within" as opposed to
"intersects". This might create unexpected results. We recommend using options 1, 2 or 3
above.Also, please note these options are mutually exclusive so you cannot pass both geojson and bounding
box options. TheOpensearch Geo Schema validatorswill raise an exception if mutually exclusive
parameters are passed.Getting geometa from an itemTo get geospatial metadata on an item, call the following endpoint:curl'{girderApiUrl}/item/{itemId}/geometa'-XGETVagrant ExamplesThere are currently2 vagrant examplesto quickly get up and running.
If you are having problems installing this plugin check ansible playbooks forubuntu-16.04andubuntu-18.04.Running testscdgeometa
pipinstall-rrequirements-dev.txt
pytest-n4
Package: girder-jupyter
The Jupyter Notebook web application provides a graphical interface for creating, opening, renaming, and deleting files in a virtual filesystem.girder_jupyteris a python package that implements acontents managerto allow Girder to become a backend for this virtual filesystem. This allows notebooks and files to be stored
in a Girder server from within Jupyter.Getting StartedInstall the package in the Python environment you are running your Jupyter server in:pipinstallgirder-jupyterAdd the following options to yourjupyter_notebook_config.pyc.NotebookApp.contents_manager_class='girder_jupyter.contents.manager.GirderContentsManager'c.GirderContentsManager.api_key='<api key>'c.GirderContentsManager.api_url='<api url>'Where<api key>is replaced with aGirder API keyfor the Girder server and<api url>is the URL to Girder instance you want
to use for examplehttp://localhost:8080/api/v1.Configuration Parametersapi_url- An API URL for the Girder server. Defaults to ‘http://localhost:8080/api/v1’api_key-AGirder API keykey for the Girder server atapi_url. The key should have read and write permission scope.token- A Girder token for the Girder server atapi_url. This parameter is particularly useful when running instances from JupyterHub.root- The root in the Girder hierarchy to use as the content managers root. This path can include{login}which will be replace with the current users login. Defaults to'user/{login}'Note that eitherapi_keyortokenmust be provided for the contents manager to be able to
authenticate with the Girder server.
Package: girder-jupyterhub
girder_jupyterhubgirder_jupyterhub is a python package that implements a JupyterHub authenticator, that
allows a user to authenticate using a Girder token.ConfigurationAdd the following options to yourjupyterhub_config.pyc.JupyterHub.authenticator_class = ‘girder_jupyterhub.auth.GirderAuthenticator’This extension usesauthentication stateto store Girder-Tokens. In production this requires the following environment variable to be set.export JUPYTERHUB_CRYPT_KEY=<key>Where <key> is the result of running:openssl rand -hex 32
Package: girder-monkeybrains
monkeybrainsmonkeybrains is a third-party, i.e. non-core, -plugin for Girder.It has the following goalsdemonstrate dataset visualization capabilities in Girdertarget a specific Collection in Girderlive on a public Girder instance without intruding on other CollectionsUsageEnable monkeybrains as a Girder plugin, then activate a specific Collection with the monkeybrains api call on a Collection, which you can do from Swagger.  This is intentionally hidden so that other Collections won't accidentally enable the functionality for them.PUT
http://localhost:8082/api/v1/collection/550701fd0640fd09bf7d6f51/monkeybrains?monkeybrains=trueOnce themonkeybrainsproperty is added to your Collection, when you edit the collection, a new component will appear belowDescriptionallowing you to add a Markdown Info Page on your Collection.  This Info Page will be rendered as Markdown at the top of your Collection page within Girder, although any inline HTML in the Markup is sanitized.A chart is also displayed on your Collection, showing a visualization of a longitudinal dataset.  This relies on an API call in the monkeybrains plugin calledgetDatasetEvents, which looks for Folders in the targeted Collection with a metadata key ofscan_date, and returns the following set of metadata on those folders_idbaseParentIdparentIdmeta.folder_typemeta.scan_agemeta.sexmeta.scan_datemeta.subject_idmeta.dobmeta.scan_weight_kgThis metadata is used to create the longitudinal display and allow mouse click events on certain parts of the display to navigate to related Girder folders.PublishingTo publish a new version of this plugin:Increment the version insetup.pyRuntox -e releaseCommit changes
Package: girder-resource-path-tools
A Girder plugin to add some server-side tools that work with resource paths.FeaturesDownload by path.GET/resource/path/download/<resourcepath>will download the collection, user, folder, item, or file.  If there is a single file within a parent object, the file will be downloaded directly.  If there are multiple files, a zip file will be downloaded.Redirect by path.GET,PUT,POST,DELETE/resource/path/redirect/<resourcepath>[/<pathcomponents>]will redirect to the appropriate model route for the last identifiable Girder model within the route.Since only routes that the user has permission for can be accessed, this can have strange repercussions if the resource path has components that look like route paths.  For instance,PUT /resource/path/redirect/user/User/Public/ItemA/metadatawill either modify an item’s metadata OR alter a file namedmetadatawithin the item.Also, redirecting has a significant overhead compared to accessing a route by model and id, as the resource path must be validated and checked for permissions.Browse files via path.AGET /filesendpoint is added at the server’s root (not under the/api/v1route).  This responds much like an ftp server, providing HTML listings of available resources (based on the current user).  If the path is a single-file item or a file, then the appropriate file is returned.  For instance/files/user/User/Public/would list folders and items within the user’sPublicfolder, while/files/user/User/Public/ItemA/File1will download the specified file.