admix | admixture analysis tool for Python that supports raw data

 by   stevenliuyi Python Version: 1.2 License: GPL-3.0

kandi X-RAY | admix Summary

kandi X-RAY | admix Summary

admix is a Python library. admix has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install admix' or download it from GitHub, PyPI.

Admix is a simple tool to calculate ancestry composition (admixture proportions) from SNP raw data provided by various DNA testing vendors (such as 23andme and AncestryDNA).
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            kandi-support Support

              admix has a low active ecosystem.
              It has 30 star(s) with 8 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 0 open issues and 2 have been closed. On average issues are closed in 105 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of admix is 1.2

            kandi-Quality Quality

              admix has no bugs reported.

            kandi-Security Security

              admix has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              admix is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              admix 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.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed admix and discovered the below as its top functions. This is intended to give you an instant insight into admix implemented functionality, and help decide if they suit your requirements.
            • Calculate the best fitting results for a list of models
            • Extract genotypes from a csv file
            • Return frequency file name for a given model
            • Name of snp file for a given model
            • Convenience function
            • Check if the file exists
            • Computes the likelihood of the distribution
            • Convenience method that parses and returns a dictionary of three - three - letter data
            • Convert ftdna2 to genotypes
            • Generate a single gene
            • Convert a TDNA file into a dictionary
            • Calculate genotype matches
            • Calculate an admix fraction
            • Read a model
            • Read raw data
            • Returns a list of population populations
            • Number of populations in a model
            • Argument parser
            • List of available models
            Get all kandi verified functions for this library.

            admix Key Features

            No Key Features are available at this moment for admix.

            admix Examples and Code Snippets

            No Code Snippets are available at this moment for admix.

            Community Discussions

            QUESTION

            activeadmin and dynamic store accessors fails on new resource
            Asked 2020-May-06 at 23:26

            I want to generate forms for a resource that has a postgres jsonb column :data, and I want the schema for these forms to be stored in a table in the database. After a lot of research I am 90% there but my method fails in ActiveAdmin forms upon create (not update). Can anyone explain this?

            Sorry for the long code snippets. This is a fairly elaborate setup but I think it would be of some interest since if this works one could build arbitrary new schemas dynamically without hard-coding.

            I am following along this previous discussion with Rails 6 and ActiveAdmin 2.6.1 and ruby 2.6.5.

            I want to store Json Schemas in a table SampleActionSchema that belong_to SampleAction (using the json-schema gem for validation)

            ...

            ANSWER

            Answered 2020-May-06 at 23:26

            SOLUTION:

            I traced what AA was doing to figure out the minimum number of commands needed. It was necessary to add code to build_new_resource to ensure that any new resource AA built had the correct :category field, and once doing so, make the call to dynamically add the store_accessor keys to the newly built instance.

            Now users can create their own original schemas and records that use them, without any further programming! I hope others find this useful, I certainly will.

            There are a couple ugly solutions here, one is that adding the parameters to the active admin new route call is not expected by AA, but it still works. I guess this parameter could be passed in some other way, but quick and dirty does the job. The other is that I had to have the form generate a session variable to store what kind of schema was used, in order for the post-form-submission build to know, since pressing the "Create Move" button clears the params from the url.

            The operations are as follows: for a model called Move with field :data that should be dynamically serialized into fields according to the json schema tables, both admin/moves/new?category="cleave" and admin/moves/#/edit find the "cleave" schema from the schema table, and correctly create and populate a form with the serialized parameters. And, direct writes to the db

            Source https://stackoverflow.com/questions/61629577

            QUESTION

            How to plot a data table of 0's and 1's as a two-color grid in R?
            Asked 2020-Apr-27 at 19:31

            I have some files like the one below. Each contains 26 lines, which consist of a sample name and a number of 0's and 1's.

            ...

            ANSWER

            Answered 2020-Apr-27 at 19:31

            Considering the following example. Based , on your code, removing as.matrix when you load the dataset should make you be able to obtain a similar structure)

            Source https://stackoverflow.com/questions/61466694

            QUESTION

            Why r shows an error when using dplyr and ifelse together?
            Asked 2020-Jan-10 at 18:40

            I am trying to use the "ifelse" function in R grouping but it doesn't work. My data is something like this:

            ...

            ANSWER

            Answered 2020-Jan-10 at 17:27

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

            Vulnerabilities

            No vulnerabilities reported

            Install admix

            You can use pip to install Admix directly from this Github repository:.

            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 admix

          • CLONE
          • HTTPS

            https://github.com/stevenliuyi/admix.git

          • CLI

            gh repo clone stevenliuyi/admix

          • sshUrl

            git@github.com:stevenliuyi/admix.git

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