hgvs | Python library to parse format validate normalize | Genomics library

 by   biocommons Python Version: 1.5.4 License: Apache-2.0

kandi X-RAY | hgvs Summary

kandi X-RAY | hgvs Summary

hgvs is a Python library typically used in Artificial Intelligence, Genomics applications. hgvs has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install hgvs' or download it from GitHub, PyPI.

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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            kandi-support Support

              hgvs has a low active ecosystem.
              It has 209 star(s) with 83 fork(s). There are 20 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 93 open issues and 497 have been closed. On average issues are closed in 266 days. There are 4 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of hgvs is 1.5.4

            kandi-Quality Quality

              hgvs has 0 bugs and 0 code smells.

            kandi-Security Security

              hgvs has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              hgvs code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              hgvs is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              hgvs releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              It has 10060 lines of code, 632 functions and 84 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed hgvs and discovered the below as its top functions. This is intended to give you an instant insight into hgvs implemented functionality, and help decide if they suit your requirements.
            • Decorator for lru_cache
            • Saves the configuration to disk
            • Normalize a variant variant
            • Get the boundary of a variant
            • Fetch a sequence from a given chromosome
            • Get the total transcript length for a given variant
            • Perform variant context w alignment
            • Generate a full house
            • Return a list of all transcripts for a variant
            • Retrieve transcript exons associated with a transcript
            • Get a cursor
            • Connect to NCBI
            • Return a function that can be used to parse a string
            • Include delins
            • Get information about a particular transcript
            • Convert a cDNA variant from a cDNA variant
            • Convert cDNA to nucleotides
            • Convert an n_to_c into a C variant
            • Get all similar transcripts for a given transcript
            • Validate a variant variant
            • Get the mapping options for a transaction
            • Retrieve transcript identity information
            • Incorporate dup sequence
            • Incorporate inv into sequence
            • Get information about a gene
            • Convert g from g to T
            • Return a list of transcripts for a variant
            Get all kandi verified functions for this library.

            hgvs Key Features

            No Key Features are available at this moment for hgvs.

            hgvs Examples and Code Snippets

            No Code Snippets are available at this moment for hgvs.

            Community Discussions

            QUESTION

            getting different patterns within the same string
            Asked 2022-Mar-03 at 10:21

            I've got the following data frame:

            ...

            ANSWER

            Answered 2022-Mar-03 at 10:21

            Here is a potential solution:

            Source https://stackoverflow.com/questions/71334906

            QUESTION

            How can I separate the information in one column of the table I have into 3 separate columns?
            Asked 2022-Feb-13 at 21:16

            For example, one column of the table I have is like this

            ...

            ANSWER

            Answered 2022-Feb-13 at 21:05
            Code

            Here is a base R way with substr.

            Source https://stackoverflow.com/questions/71104772

            QUESTION

            How can I separate 3 different information in a column?
            Asked 2022-Feb-12 at 16:58

            For example, in the column I have, there is a line written 'Ser25Phe'. And I want to split the column HGVS.Consequence e.g. as 'Ser 25 Phe'...

            ...

            ANSWER

            Answered 2022-Feb-12 at 11:29

            Using gsub, assuming that e.g. "AsAsp" should also be split into "As Asp".

            Source https://stackoverflow.com/questions/71089487

            QUESTION

            How to append list to list using python?
            Asked 2021-Nov-24 at 07:20

            I wonder to append listB to listA

            input

            ...

            ANSWER

            Answered 2021-Nov-24 at 06:07

            listA.extend(listB) should work, but it modifies the original listA. If you want sum_list to be a different list, you can copy it first with something like

            Source https://stackoverflow.com/questions/70091384

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install hgvs

            You can install using 'pip install hgvs' or download it from GitHub, PyPI.
            You can use hgvs like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            Install
          • PyPI

            pip install hgvs

          • CLONE
          • HTTPS

            https://github.com/biocommons/hgvs.git

          • CLI

            gh repo clone biocommons/hgvs

          • sshUrl

            git@github.com:biocommons/hgvs.git

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