Saravanan666/pypi-org huggingface dataset:
Package: umiread
umireadumiread is a lightweight utility that allows for seamless parsing of R1 FASTQ files generated from 10x single cell 3' gene expression assays. The functions contained within this package show the user very important baseline quality control metrics about the unique molecular identifiers (UMIs) contained within one or more R1 FASTQs, including total number of unique and non-unique sequences, nucleotide distribution, and basecalling errors. umiread can be used for preliminary parsing of 10x single cell FASTQ files prior to downstream analysis.
For more information on 10x single cell 3' gene expression assays, visithttps://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sequencing-requirements-for-single-cell-3Installation & Dependenciesumiread requires the following packages:- pandas

- numpy

- matplotlibIn PyCharm or another Python IDE (Python 3 or greater), installation can be completed as follows:pip install umireadReading & Extracting from FASTQ filesumiread has the ability to parse one or more R1 FASTQ files from a 10x 3' single cell assay (any version).For parsing a single FASTQ file:from umiread import extract_from_single
umi_data = extract_from_single("path/to/FASTQ file/~.fastq.gz")For parsing multiple FASTQ files contained within the same folder (i.e. multiple FASTQs corresponding to the same sample):from umiread import extract_from_folder
umi_data = extract_from_folder("path/to/FASTQ folder/")The parser will collect the 10bp UMI at the beginning of each R1 sequence contained within the targeted FATSQ files. Assigning the parsed sequences to an object such as umi_data will allow for the user to generate quality control metrics.Collecting Quality Control Metrics & Sequencing ErrorsHaving information about the total number of UMI sequences, unique UMI sequences, and nucleotide distribution can be useful for tracking the quality of wet lab workflows and overall data quality before downstream applications and further data analysis. umiread possesses a handful of functions that can print these statistics to console.For basic statistics such as total number of UMIs, unique UMIs, percentage of UMIs that are unique, and the number of UMIs with a sequencing error, use the following command:from umiread import UMIStats
UMIStats(umi_data).collect_qc_statistics()This function will output a simple csv with all aforementioned QC metrics.For nucleotide distributions (i.e. the number of A, C, T, G in all unique UMIS):UMIStats(umi_data).base_distribution()For a graph of the positional distribution of sequencing errors in the UMI (denoted by "N" in the FASTQ file):UMIStats(umi_data).show_seq_errors()
Package: umirobot
UMIRobot PythonThe Python package to interact with the UMIRobot.Citation:@misc{marinho2022umirobot,author={Marinho, M. M. and Lin, H. and Zhao, J.},title={UMIRobot: An Open-{Software, Hardware} Low-Cost Robotic Manipulator for Education},booktitle={2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)},year={2023},month=oct,organization={IEEE},custom_type={2. International Conference Paper},pages={1--8},note={Accepted for publication.},url={https://arxiv.org/pdf/2302.05567},url_code={https://github.com/mmmarinho/umirobot-py},url_website={https://mmmarinho.github.io/UMIRobot/}}General User - GUI VersionDownload the latest binaries athttps://github.com/mmmarinho/umirobot-py/releases/latestand run it.Tested on:Windows 10/11MacOS (Intel/M1)ProgrammerNOTE:The package is only compatible with Python >= 3.8.InstallationUsepipto install the package. Dependencies will be automatically installed.python -m pip install umirobotUpgradepython -m pip install umirobot --upgradeUsageYou can run the GUI as followspython -m umirobotFor more advanced usage, seehttps://github.com/mmmarinho/umirobot
Package: umk
Unimakeunimakeis a set of development tools and frameworks for project maintaining. This tools makes it easy to organize development routines (such as building, testing, linting, running, etc) for a specific code base.GoalsAllow gophers to use the full power of Python instead of makefiles and shell scripts.Facilitate the task of product building consisting of several projects in different languages.Provide the opportunity to develop debuggable project maintenance scripts.Automate project maintenance routines.FeaturesConvenient framework for a project descriptionPython is the only language for everythingDebuggable pipeline (unlike regular shell scripts)Easiest way to create a powerful CLI (likemakebut more flexible)Adapters for a commonly used build systems (go,cmake, ...)Run project targets in remote environment (dev-container, remote server, etc)How it works ?Unimake provides the Python framework (umk), project commands runner tool (umk cli) and command line manager (unimake).A specific project must contain at least 2 scripts:.unimake/project.py- project info, build steps, etc..unimake/cli.py- command line interface to interact with projectumktool allows you to execute a command from.unimake/cli.pyScript project.pyimportumkclassProject(umk.GoProject):def__init__(self):super().__init__()self.git=umk.git()self.info.name.short="project-name"self.info.name.full="Project Name"self.info.version=umk.tag(self.git,"v1.0.0")self.info.authors=[umk.Author('Author Name','author.name@email.com')]self.info.description="Super puper mega description"self.go=umk.Go.find("1.19")self.dlv=umk.Delve.find()asyncdefbuild(self,mode:str):args=umk.GoBuildArgs.new(mode)args.output=self.layout.output/'foo'args.sources.append(self.layout.cmd/'foo')args.flags.go.append('-mod=vendor')awaitself.go.build(args).asyn()defvendor(self):self.go.mod.tidy().sync()self.go.mod.vendor().sync()defdebug(self,port=2345):self.dlv.exec(binary=self.layout.output/'foo',flags=umk.DelveFlags(port)).sync()project=Project()Script cli.pyfromumkimportclifromprojectimportproject@cli.cmd()defvendor():project.vendor()@cli.cmd()@cli.opt('--mode',default='debug',help='Build mode (debug|release)')asyncdefbuild(mode:str):awaitproject.build(mode)@cli.cmd(help="Run debug server (on port 2345 by default)")@cli.opt('--port',type=int,default=2345)defdebug(port:int):project.debug(port)Execute projects commandcdpath/to/project/root
umkvendor
umkbuild
umkdebug--port3000InstallationSeeinstallation instructionsfor more details.DocumentationIntoductionTool: umk
Package: uml2django
uml2django is a tool for generateDjangocode fromPlantUML class diagrams.
It able to generate:ModelsFormsClass Based ViewsTemplatesTestsQuick startInstallationInstall via pip:pip install uml2djangoDownload from github:git clone https://github.com/J-hanks/uml2djangoRunningFrom command line:uml2django --puml my_plant_uml_class_diagram.pumlImport as script:from uml2django.settings import settings
from uml2django import objects
from uml2django import load_data_from

PLANT_UML_FILE = "school_management_project.puml"
load_data_from(plantuml_file_path=PLANT_UML_FILE)
for django_model in objects.DJANGO_MODELS:
    django_model.generate_model_python_file()
    if not django_model.is_abstract:
        django_model.generate_rest_api()
        django_model.generate_model_forms()
        django_model.generate_class_based_views()
        django_model.generate_cbv_urls_routing()
        django_model.generate_templates()SyntaxAppsTo represent an Django App, use the PlantUMLpackagetag.The app name must followpep8:Modules and packages should have short, all-lowercase names.Underscores can be used if it improves readability,although the use of underscores is discouraged.:@startuml
    package exampledjangoapp {

    }
    package example_django_app {

    }
@endumlModelsUse PlantUMLclasstag to represent an Django Model.The Model name must followpep8:where stands that class names should normally use the CapWords convention.All classes defined MUST BE inside an package, like models inside Django apps.:@startuml
    package exampledjangoapp {
        class MyFirstModel {

        }
    }
    package example_django_app {
        class MySecondModel {

        }
    }
@endumlModels InheritanceMeta inheritance@startuml
    package exampledjangoapp {
        abstract class BaseModel {
            {field} name : CharField(max_length=30)
        }
        class ExtendedModel {
            {field} name : CharField(max_length=30)
        }
        BaseModel <-- ExtendedModel : inherit
    }
@endumlMulti-table inheritanceProxy inheritanceModels RelashionshipsMany-to-oneMany-to-manyOne-to-oneModel FieldsUse PlantUML{field}tag to represent an Django model field.If the field type is not informed, uml2django define it as CharField.:@startuml
    package exampledjangoapp {
        class MyFirstModel {
            {field} char_field : CharField(max_length=30)
            {field} other_char_field
        }
    }
    package example_django_app {
        class MySecondModel {
            {field} integer_field : IntegerField()
        }
    }
@enduml
Package: uml2py
A converter from PlantUML class diagrams to python3 skeleton classessupported PlantUML class diagram syntax:` uml : "@startuml" decls "@enduml" decls : ε | decls decl decl : class | assoc | "skinparam" class : abs "class" id '{' attribs '}' class : abs "interface" id '{' attribs '}' abs : ε | "abstract" attribs : ε | attribs attrib attrib : prot id vec type init attrib : prot id '(' ')' type attrib : prot id '(' args ')' type attrib : prot "static" id '(' ')' type attrib : prot "static" id '(' args ')' type attrib : prot "abstract" id '(' ')' type attrib : prot "abstract" id '(' args ')' type type : ε | ':' id vec args : id type | args ',' id type prot : ε | '+' |'-'| '~' | '#' vec : ε | '[' ']' | '['[0-9]+']' |'<[_A-Za-z][A-Za-z0-9_]*>'init : ε | '=' id | '=' str | '='[0-9]+assoc : id('<|--'|'<|..'|'--|>'|'..|>')id assoc : id card('*-->'|'--*'|'<--*'|'o-->'|'o--'|'<--o'|'--o'|'-->'|'<--'|'--')card id type card : ε | STR str :'"([^"\\]|\\.)*"'id :'[_A-Za-z][A-Za-z0-9_]*'`comments start with#symbol and end the end of the line.A simple class example:` @startuml skinparam classAttributeIconSize 0 skinparam monochrome true class Tire { - _pressure: int - _standard: int - _flat: bool--+ Tire(standard: int , pressure: int) + standard() : int + pressure() : int + flat() : bool + pressure(pressure: int) : void + empty() : bool } @enduml `Generate the python3 skeleton code tostdoutwith:` python3-muml2py tire.uml `or save the skeleton code to a file:` python3-muml2py tire.uml tire.py `Use the environmentDEBUG=1for a verbose output:` DEBUG=1 python3-muml2py tire.uml `Some examples in theexamples/directory.prs, IST 2022
Package: umlify
UMLify PythonUMLify Python is a library that allows generating UML (Unified Modeling Language) diagrams in plantUML format from Python code. This tool is particularly useful for visualizing the structure and relationships in Python projects, aiding in understanding and documenting complex systems.FeaturesCurrently, UMLify supports the generation of class diagrams, with plans to expand to other types of UML diagrams. Initially, it was developed with a focus on Django projects, but it is evolving to support a broader range of Python code structures and frameworks.InstallationTo install UMLify, use the following command:pipinstallumlifyUsageTo generate a UML diagram, follow the steps below:Import thegenerate_class_diagramfunction from the UMLify module.fromumlify.class_diagramimportgenerate_class_diagramDefine the path to your Python project and the names of the packages you wish to analyze.app_path='/path/to/your/project'package_names=["views","services","repositories"]# Example packagesCall thegenerate_class_diagramfunction with the project path, package names, and the output file path.output_file='/path/to/diagram.puml'generate_class_diagram(app_path,package_names,output_file)LicenseUMLify is licensed under theMIT License.
Package: uml-interpreter
AboutThe aim of UML Interpreter project is to enable simple interaction with UML diagrams using Python code.The main motivation behind this project is to provide a convinient way to modify UML Diagrams using scripts written in
high-level programming languages rather than manually interact with them using graphical editors.RequirementsPython 3.10+Installationpip install uml-interpreterDev Usagemake setup: installs all dependenciesmake test: runs pytest testsmake tox-test: runs tox testsmake docs: serves documentation at localhostmake docs-build: builds docsmake export: exports dependencies to requirements.txtmake publish: - publishes the package to PyPImake publish-test: - publishes the package to Test PyPImake clean: - cleans working directoryLicenseThis project is licensed under the terms of the MIT license.AuthorsFilip PawłowskiHubert SorokaMaciej Tymoftyjewicz
Package: umls-api
umls-apiPython client forhttps://documentation.uts.nlm.nih.gov/rest/home.htmlInstallationpipinstallumls-apiExample UsageGet CUI.importumls_apiresp=umls_api.API(api_key='<UMLS_API_KEY_HERE>').get_cui(cui='C0007107')print(res){'pageCount':1,'pageNumber':1,'pageSize':25,'result':{'atomCount':247,'atoms':'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/atoms','attributeCount':0,'classType':'Concept','cvMemberCount':0,'dateAdded':'09-30-1990','defaultPreferredAtom':'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/atoms/preferred','definitions':'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/definitions','majorRevisionDate':'06-25-2020','name':'Malignant neoplasm of larynx','relationCount':17,'relations':'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/relations','semanticTypes':[{'name':'Neoplastic Process','uri':'https://uts-ws.nlm.nih.gov/rest/semantic-network/2020AB/TUI/T191'}],'status':'R','suppressible':False,'ui':'C0007107'}Get TUI.importumls_apiresp=umls_api.API(api_key='<UMLS_API_KEY_HERE>').get_tui(cui='T047')print(resp){'pageCount':1,'pageNumber':1,'pageSize':25,'result':{'abbreviation':'dsyn','childCount':2,'classType':'SemanticType','definition':'A condition which alters or interferes with a ''normal process, state, or activity of an organism. ''It is usually characterized by the abnormal '"functioning of one or more of the host's systems, "'parts, or organs. Included here is a complex of ''symptoms descriptive of a disorder.','example':'NONE','name':'Disease or Syndrome','nonHuman':'NONE','semanticTypeGroup':{'abbreviation':'DISO','classType':'SemanticGroup','expandedForm':'Disorders','semanticTypeCount':12},'treeNumber':'B2.2.1.2.1','ui':'T047','usageNote':'Any specific disease or syndrome that is modified by ''such modifiers as "acute", "prolonged", etc. will ''also be assigned to this type. If an anatomic ''abnormality has a pathologic manifestation, then it ''will be given this type as well as a type from the '"'Anatomical Abnormality' hierarchy, e.g., "'"Diabetic Cataract" will be double-typed for this ''reason.'}}If you wish to add support for other API endpoints on UMLS, they are very simple to add.Pull requests (with tests) are very welcome.Running the testspipinstall-rrequirements-dev.txt
pytestsrc/tests
flake8Release History0.1.0 (2020-12-01)Initial release.
Package: umls-api-client
umls-apiClass to interact with the UMLS APIDocumentation will be added later, for now refer to theAPIsdocumentation. Each endpoint maps to a function in the class.CreditsAuthor:Naveen JayakodyUMLS Citation:Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D267-70. doi: 10.1093/nar/gkh061. PubMed PMID: 14681409; PubMed Central PMCID: PMC308795.Read the full textUMLS API Technical Documentation
Package: umls-client
umls-clientpython umls clientDescriptionlight umls client with rate limitingInstallationpip install umls-clientUsageresolver = UMLSClient("API_KEY")
r0 = resolver.search_string("olfactory receptor")
print(r0.result)
r0.has_next_page() # True
r0_a = resolver.search_string("olfactory receptor", page=99)
r0_a.has_next_page() # False

r1 = resolver.search_cui("C1518565")
# r1.result = {...}
r2_a = resolver.search_cui("C1518565", CuiExtension.RELATIONS)
# r2_a.result = [{...},{...},{...}]
r3 = resolver.search_tui("T104")
# r3.result = {...}Roadmap- [x] GET 	/search/{version}                                       Retrieves CUIs when searching by term or code
  - [x] GET 	/content/{version}/CUI/{CUI} 	                        Retrieves information about a known CUI
  - [x] GET 	/content/{version}/CUI/{CUI}/atoms                      Retrieves atoms and information about atoms for a known CUI
  - [x] GET 	/content/{version}/CUI/{CUI}/definitions             	Retrieves definitions for a known CUI
  - [x] GET 	/content/{version}/CUI/{CUI}/relations              	Retrieves NLM-asserted relationships for a known CUI
  - []  GET 	/content/{version}/source/{source}/{id}                 Retrieves information about a known source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/atoms           Retrieves information about atoms for a known source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/parents     	Retrieves immediate parents of a source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/children    	Retrieves immediate children of a source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/ancestors   	Retrieves all ancestors of a source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/descendants 	Retrieves all descendants of a source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/relations       Retrieves all relationships of a source-asserted identifier
  - []  GET 	/content/{version}/source/{source}/{id}/attributes      Retrieves information about source-asserted attributes
  - [x] GET 	/semantic-network/{version}/TUI/{id} 	                Retrieves information for a known Semantic Type identifier (TUI)
  - []  GET 	/crosswalk/{version}/source/{source}/{id}               Retrieves all source-asserted identifiers that share a UMLS CUI with a particular codeAuthors and acknowledgmenthttps://documentation.uts.nlm.nih.gov/rest/home.htmlhttps://requests.readthedocs.io/en/latest/
Package: umls-downloader
UMLS DownloaderDon't worry aboutUMLS Terminology Services (UTS)licensing and distribution rules - just useumls_downloaderto write code that knows how to download content and use it
automatically from the following (non-exhaustive) list of resources:UMLSRxNormSemMedDBSNOMED-CTpotentially more in the futureor any content that can be downloaded through
theUTS ticket grantingsystem. There's no centralized list of content available through the UTS so
suggestions for additional resources are welcome through
theissue tracker.Full documentation are available atumls-downloader.readthedocs.io.Installation$pipinstallumls_downloaderDownload A Specific Version of UMLSimportosfromumls_downloaderimportdownload_umls# Get this from https://uts.nlm.nih.gov/uts/edit-profileapi_key=...path=download_umls(version="2021AB",api_key=api_key)# This is where it gets downloaded: ~/.data/bio/umls/2021AB/umls-2021AB-mrconso.zipexpected_path=os.path.join(os.path.expanduser("~"),".data","umls","2021AB","umls-2021AB-mrconso.zip",)assertexpected_path==path.as_posix()After it's been downloaded once, it's smart and doesn't need to download again.
It gets stored usingpystowautomatically
in the~/.data/bio/umlsdirectory.A full list of functions is available in thedocumentation.Automating Configuration of UTS CredentialsThere are two ways to automatically set the username and password so you don't
have to worry about getting it and passing it around in your python code:SetUMLS_API_KEYin the environmentCreate~/.config/umls.iniand set in the[umls]section aapi_keykey.fromumls_downloaderimportdownload_umls# Same path as beforepath=download_umls(version="2021AB")Download the Latest VersionFirst, you'll have to
installbioversionswithpip install bioversions, whose job it is to look up the latest version of
many databases. Then, you can modify the previous code slightly by omitting
theversionkeyword argument:fromumls_downloaderimportdownload_umls# Same path as before (as of November 21st, 2021)path=download_umls()Download and open the fileThe UMLS file is zipped, so it's usually accompanied with the following
boilerplate code:importzipfilefromumls_downloaderimportdownload_umlspath=download_umls()withzipfile.ZipFile(path)aszip_file:withzip_file.open("MRCONSO.RRF",mode="r")asfile:forlineinfile:...This exact code is wrapped with theopen_umls()using Python's context manager
so it can more simply be written as:fromumls_downloaderimportopen_umlswithopen_umls()asfile:forlineinfile:...Theversionandapi_keyarguments also apply here.Why not an API?The UMLS provides anAPIfor access to tiny bits of data at a time. There are even two recent (last 5
years) packagesumls-apiconnect-umlsthat provide a wrapper
around them. However, API access is generally rate limited, difficult to use in
bulk, and slow. For working with UMLS (or any other database, for that matter)in
bulk, it's necessary to download full database dumps.👋 Attribution⚖️ LicenseThe code in this package is licensed under the MIT License.🍪 CookiecutterThis package was created
with@audreyfeldroy'scookiecutterpackage
using@cthoyt'scookiecutter-snekpacktemplate.
Package: umls-graph
UMLS-GraphBuild a medical knowledge graph based on Unified Language Medical System (UMLS)RequisiteInstall MySQL Server 5.6 and import UMLS data into MySQL database. Please refer toUMLSwebsites on how to install the UMLS database.Installationpip install umls-graphLet Codes Speakfromumls_graph.datasetimportmake_umls_all# MySQL database informationmysql_info={}mysql_info["database"]="umls"mysql_info["username"]="root"mysql_info["password"]="{not gonna tell you}"mysql_info["hostname"]="localhost"# read all UMLS table and save them to csv formatted files in a specific foldermake_umls_all(mysql_info=mysql_info,save_folder="umls_datasets")LicenseTheumls-graphproject is provided byDonghua Chen.NOTE: This project DOES NOT provide the UMLS data download due to the license issue. In addition, the processed data are not verified in actual clinical use.  Please be response for any UMLS data use.
Package: umls-rat
UMLS RATUMLS RAT (RESTAPITool) provides a reasonable interface to theUMLS Metathesaurusvia theREST API. We cache responses usingrequests cacheto speed things up. Ultimately, you will only end up downloading as much data as youneedwhich for most use cases is a relatively small portion of the whole. If you need the entire Metathesaurus, this is not the best tool.Installpip install umls-ratLinksLatest documentation.Source on Github.
Package: umltodjango
# UML2DJANGO# Introduction# Dependencies
- XMLhttps://docs.python.org/3.8/library/xml.etree.elementtree.html#module-xml.etree.ElementTree- UMLhttps://github.com/jgraph/drawio-desktop/releases/tag/v20.3.0# Features
- model inheritance tree dependencies# Installation# Usage# TODO’s
- attributes params
- write relations
- django model type relations
- parse from draw.io xml or plantuml