All2 | filtering variants from all2all comparison | Genomics library

 by   abyzovlab Python Version: Current License: MIT

kandi X-RAY | All2 Summary

kandi X-RAY | All2 Summary

All2 is a Python library typically used in Artificial Intelligence, Genomics, Tensorflow applications. All2 has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However All2 build file is not available. You can download it from GitHub.

A tool for filtering variants from all2all comparison of multiple clones or single cells.
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            kandi-support Support

              All2 has a low active ecosystem.
              It has 2 star(s) with 0 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              All2 has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of All2 is current.

            kandi-Quality Quality

              All2 has 0 bugs and 0 code smells.

            kandi-Security Security

              All2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              All2 code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              All2 is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              All2 releases are not available. You will need to build from source code and install.
              All2 has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              It has 1319 lines of code, 37 functions and 2 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed All2 and discovered the below as its top functions. This is intended to give you an instant insight into All2 implemented functionality, and help decide if they suit your requirements.
            • Extract mutation information from a manifest file .
            • Generate an explanation for an explanation .
            • Extract mutation information from a VCF file .
            • Validate a file
            • Validates that a directory exists .
            • Ensures that f exists .
            Get all kandi verified functions for this library.

            All2 Key Features

            No Key Features are available at this moment for All2.

            All2 Examples and Code Snippets

            No Code Snippets are available at this moment for All2.

            Community Discussions

            QUESTION

            Append a dictionary array to another dictionary array in Swift
            Asked 2022-Mar-02 at 08:20

            I have two quote dictionaries I'm trying to append after an in-app purchase. I have tried several different methods to append the dictionaries together but I'm still getting an error "No exact matches in call to instance method 'append'"

            I have established variables for each array to then append the array within the struct.

            Any thoughts? Is there a better method I should use to add the quotes from the array called QuoteDetails2 to the initial array QuoteDetails?

            ...

            ANSWER

            Answered 2022-Mar-02 at 03:36

            This should be a comment but it would be a bit tricky to explain what Koropok & Leo Dabus were saying without the formatting.

            You have two arrays:

            Source https://stackoverflow.com/questions/71316231

            QUESTION

            Building binary with not default target 'all' in Makefile
            Asked 2022-Feb-18 at 19:15

            I have simple Makefile below. That runs clear when using default target all.

            ...

            ANSWER

            Answered 2022-Feb-18 at 19:15

            The reason is that make has a built-in rule that knows how to build a binary file from an object file that has the same prefix; that is, given a binary file foo make has a built-in rule that knows how to build it from foo.o.

            You have a target all2 and normally that doesn't matter because you don't have an all2.c and so make can't find a way to build all2.o and so it decides there's no rule to build all2.

            But in your makefile, you've created a rule to build any .c file, so when make tries to find a way to build all2.o it discovers it can be built from all2.c and there is a rule to build all2.c, so the rule matches.

            Of course, you won't have a rule like %.c : ; touch $@ in your non-test makefile so you won't see this problem in any real makefile.

            If you want to make this work for your test environment you can, as @Cheatah says, declare the all2 rule to be phony which will prevent make from trying to look up any rules to build it.

            Source https://stackoverflow.com/questions/71177178

            QUESTION

            How can I order these bars using ggplot? Why is the forcat method not working?
            Asked 2022-Feb-14 at 07:22

            I'm trying to reorder the bars on my bargraph so they are biggest to smallest, ordered by log(Max_N) rather than alphabetically. I've tried using forcats but it brings up an error message. This is my code so far, whats going wrong? I'm trying to teach myself how to use ggplot, so please do point out any errors I've made, because I am self-taught!

            ...

            ANSWER

            Answered 2022-Feb-14 at 07:22

            Acutally if I were you, I will just have a reorder inside ggplot(aes()), then you don't need to change anything in your data.

            If you want to plot this bar chart that sum up all Max_N within a species, you can do a group_by and summarise before piping into ggplot. This will NOT change your original all dataframe.

            Source https://stackoverflow.com/questions/71100060

            QUESTION

            Load a json url from Webclient
            Asked 2022-Jan-25 at 14:21

            ANSWER

            Answered 2022-Jan-25 at 14:21

            Per default HttpClient won't send any User-Agent and this will make quite a few sites suspious. I tried the same request without setting an User-Agent header and it returned an HTML document instead.

            So you need to add a User-Agent header and it will probably work (and to be a good sport, add a user-agent that identifies your application).

            Source https://stackoverflow.com/questions/70849748

            QUESTION

            How to get the correct data in Retrofit
            Asked 2021-Aug-19 at 21:07

            I have JSON model,

            ...

            ANSWER

            Answered 2021-Aug-19 at 21:07

            I think that is a map of defined objects, but every legend is undefined

            Source https://stackoverflow.com/questions/68853432

            QUESTION

            Dividing sequential column values with a specific data frame cell in R-Updated
            Asked 2021-Jun-20 at 23:49

            Updated below

            I have a 1000 row and 780 column data frame in the following format -

            E1 P1 All1 E2 P2 All2 100 200 999 300 400 888 5 6 7 8 9 10 11 12 13 14 15 16

            I have to divide every row value (row 2-1000) in E1, P1 and All1 by first row of All1; E2, P2 and All2 by first row of All2 and so on.

            The result that I need is (table values only for illustration, i need the actual values) -

            E1 P1 All1 E2 P2 All2 5/999 6/999 7/999 8/888 9/888 10/888 11/999 12/999 13/999 14/888 15/888 16/888

            What function can be used or how to make a loop for this problem?

            Update on the format of data frame

            Column names are in the following pattern -
            Origin_Destination_Airline_Class
            for example : NYC_LAX_AA_E
            All combinations of Origin_Destination_Airline have 3 columns each for the classes (E, P, All).

            Updated table format

            NYC_LAX_AA_E NYC_LAX_AA_P NYC_LAX_AA_All DNW_SFO_DL_E DNW_SFO_DL_P DNW_SFO_DL_All 100 200 999 300 400 888 5 6 7 8 9 10 11 12 13 14 15 16

            Result needed:

            NYC_LAX_AA_E NYC_LAX_AA_P NYC_LAX_AA_All DNW_SFO_DL_E DNW_SFO_DL_P DNW_SFO_DL_All 5/999 6/999 7/999 8/888 9/888 10/888 11/999 12/999 13/999 14/888 15/888 16/888 ...

            ANSWER

            Answered 2021-Jun-20 at 23:49

            We can use tidyverse

            1. Loop across all the columns (everything()) in summarise
            2. Get the column name - cur_column()
            3. Replace the substring i.e. all non-digit in the column names with 'All'
            4. Use get to return the value of that column, subset the first -[1] element
            5. Divide the subset of rows - excluding the first row with 4

            Source https://stackoverflow.com/questions/68060363

            QUESTION

            using delcaration to inherit constructors from all base classes given by variadic template arg
            Asked 2021-May-16 at 17:02

            If I derive from one or more classes I can inherit the constructors with the using declaration.

            Example:

            ...

            ANSWER

            Answered 2021-May-16 at 17:02
            template < typename ... P>
            struct All2: public P...
            {
                using P::P...;
            };
            

            Source https://stackoverflow.com/questions/67559345

            QUESTION

            How to remove mammography tag artifacts
            Asked 2021-Apr-25 at 18:41

            I have a mammography image dataset (mini DDSM). These images show letter artifacts indicating left or right mamma and other useless information for my ML model, so I want to curate this dataset before training the model.

            In this paper, Preprocessing of Digital Mammogram Image Based on Otsu’s Threshold, they use Otsu's binarization and opening on the mammography to clean the image (page 5 of 10):

            Their results

            So far, I have coded this:

            ...

            ANSWER

            Answered 2021-Apr-25 at 18:41

            Here is one way to process your image in Python/OpenCV.

            Source https://stackoverflow.com/questions/67227335

            QUESTION

            React Native Picker - Styling selector to not be grey
            Asked 2021-Feb-06 at 08:20

            I am trying to style the selector background in the picker component, Where there is the grey background in the picture below. I am trying to change it to a white background and have a border around it.

            ...

            ANSWER

            Answered 2021-Feb-06 at 08:20

            From the issues in react-native-picker, there is a talking about the customizing the selected item inside the picker.

            More over, it is not possible to do so at present, as the native properties for the selection indicator styles aren't bridged over yet.

            The code inside RNPicker.m file should be modified to handle the customization.

            Source https://stackoverflow.com/questions/65537716

            QUESTION

            Excel VBA - delete cell with time value less then
            Asked 2021-Jan-25 at 18:21

            I'm trying to delete specific range based on a time value in the column "J" . So far I got this:

            ...

            ANSWER

            Answered 2021-Jan-25 at 18:21

            When you delete the row that contains the range czas you also delete that range object. A null range has no property .value which is why you are getting an object required error.

            A good way to mass delete range object is to use union to create non-contiguous ranges and then delete them all at once. This spares you the weirdness of shifting rows in a loop and also will significantly improve speed as deleting is pretty expensive.

            Source https://stackoverflow.com/questions/65888567

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

            Vulnerabilities

            No vulnerabilities reported

            Install All2

            You can download it from GitHub.
            You can use All2 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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            https://github.com/abyzovlab/All2.git

          • CLI

            gh repo clone abyzovlab/All2

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            git@github.com:abyzovlab/All2.git

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