mavis | Merging , Annotation , Validation , and Illustration | Genomics library

 by   bcgsc Python Version: 3.1.2 License: GPL-3.0

kandi X-RAY | mavis Summary

kandi X-RAY | mavis Summary

mavis is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. mavis 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 mavis' or download it from GitHub, PyPI.

MAVIS is python command-line tool for the post-processing of structural variant calls. The general MAVIS pipeline consists of six main stages.
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            kandi-support Support

              mavis has a low active ecosystem.
              It has 65 star(s) with 13 fork(s). There are 14 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 30 open issues and 130 have been closed. On average issues are closed in 58 days. There are 3 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of mavis is 3.1.2

            kandi-Quality Quality

              mavis has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              mavis 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

              mavis releases are available to install and integrate.
              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.
              mavis saves you 17108 person hours of effort in developing the same functionality from scratch.
              It has 33957 lines of code, 1766 functions and 128 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed mavis and discovered the below as its top functions. This is intended to give you an instant insight into mavis implemented functionality, and help decide if they suit your requirements.
            • Main function
            • Assemble a contig
            • Convert a txt file to a dictionary
            • Align sequences
            • Select contig alignment based on the query
            • Find the shared breakpoint sequence for the breakpoint
            • Calculate reference count based on repeat length
            • Create a scatter plot from a BAM file
            • Finds events from source evidence
            • Given a list of BreakpointPairs and a list of BreakpointPairs
            • Return a set of SV type from the given pair
            • Compare two inferred sequences
            • Convert a gff3 file into a pandas DataFrame
            • Parse command line arguments
            • Check options for overlays
            • Find the pair of breakpoint pairs
            • Convert mavis_2to2to2to2to3
            • Return the PAIRINE state
            • Calculate reference counts for each breakpoint pair
            • Calculate ref counts from input files
            • Assemble the contig
            • Convert a tab file to a dictionary
            • Align sequences of sequences
            • Select contig alignment based on query
            • Find the shared breakpoint sequence from the breakpoint
            • Return a row of the breakpoint pairs
            • Return a row of the table
            • Convert a BAM file into a scatter plot
            • Given a breakpoint and a list of breakpoint pairs return a list of annotation
            • Find events from source evidence
            • Determine a set of SV types
            • Check if two inferred events are equivalent
            • Given a list of annotation tuples return a list of transcripts
            • Calculate transcript priority
            • Convert a gff3 file into a pandas dataframe
            • Parse command line arguments
            • Check options
            • Find the breakpoint pairs for each breakpoint
            • Convert MASS_2to_3to_3to_2to2to_3to_3to_3to_to_3to_3to_3to_3
            • Build the JSON file
            • Return a list of domains for the given eid
            • Determine the pairing state
            • Calculate ref counts for each input
            Get all kandi verified functions for this library.

            mavis Key Features

            No Key Features are available at this moment for mavis.

            mavis Examples and Code Snippets

            Getting Started
            Pythondot img1Lines of Code : 7dot img1License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            pip install -U setuptools pip
            pip install mavis_config  # also installs snakemake
            
            snakemake \
                -j  \
                --configfile  \
                --use-singularity \
                -s Snakefile
              
            Getting Help
            Pythondot img2Lines of Code : 2dot img2License : Strong Copyleft (GPL-3.0)
            copy iconCopy
            mavis -h
            
            mavis cluster -h
              

            Community Discussions

            QUESTION

            org.springframework.security.web.access.AccessDeniedException: Access is Denied
            Asked 2021-Jun-14 at 02:53

            dispatcher-servlet.xml

            ...

            ANSWER

            Answered 2021-Jun-14 at 02:53

            This issue is solved after correcting up my code

            Source https://stackoverflow.com/questions/67764058

            QUESTION

            Doctrine ORM not working with the Migrations
            Asked 2021-Mar-08 at 00:28

            Good Day, my friends.

            I want to use the doctrine ORM with the Migrations.

            The issue is next: I want to place the migration configuration file in the specific folder. For example: 'config/doctrine-migrations.php'.

            Everything working fine when I follow the official documentation and place the migrations.php file in the root folder, but when I try to place it in the specific folder system is not working.

            My cli-config.php content is:

            ...

            ANSWER

            Answered 2021-Mar-08 at 00:28

            Looks like I found an answer.

            I can add custom integration in my application by this guide: https://www.doctrine-project.org/projects/doctrine-migrations/en/3.0/reference/custom-integration.html

            In a custom file, I can configure whatever I want.

            Hope that this solution will help somebody else.

            Source https://stackoverflow.com/questions/66522264

            QUESTION

            Dividing the large file into smaller chunks after specific character, in python?
            Asked 2020-Jul-02 at 20:45

            I'm trying to read a big file (1.1GB) into python. There will be word 'HERE' in the file. I don't know on which line I'll find the word. I read the file into chunks. My first chunk is data upto word 'HERE'. My code is working fine till here. (that is storing the data before 'HERE' and processing it) However I'm unable to proceed with reading the data after 'HERE' because the data after 'HERE' is too large. Is there any way so that I can read the data after 'HERE' line by line? I referred to the reference: Reading a file until a specific character in python My code is:

            ...

            ANSWER

            Answered 2020-Jul-02 at 20:30

            As I understood the question It think you want to separate a text file into smaller chunks in python on HERE marks in the txt file, if what I said is true try this

            Source https://stackoverflow.com/questions/62704378

            QUESTION

            How to parse JSON information then select information and assign it to a variable in Swift
            Asked 2020-May-05 at 06:44

            I am working on an app that reads a public JSON for Bike availability and many other data.

            Structs located here:

            ...

            ANSWER

            Answered 2020-May-05 at 06:19

            Here is how you can proceed.

            Let's assume you want to fetch stationName from stations array,

            Source https://stackoverflow.com/questions/61606404

            QUESTION

            Gremlin relationship recommendations
            Asked 2020-Apr-23 at 13:07

            I am trying to identify missing relationships in a graph and provide recommendations to add a user to group since his peers are in the same group. Example: Manager dave of IT has members with relationship to group. I would like to find all vertex that are sharing the same organization or manager but are not in that group.

            script example:

            ...

            ANSWER

            Answered 2020-Apr-22 at 13:25

            If you want to identify the missing relationships you can do something like this:

            Source https://stackoverflow.com/questions/61364355

            QUESTION

            populate array into input box Angular
            Asked 2020-Apr-08 at 00:15

            I'm working on a task I'm assigned to generated 10 different input forms and create an array of 10 users and loop them to fill the input box with Angular.

            So at the end of the day, I'll have 10 input forms containing the array of data

            but im getting only the last data in the array information in all the forms.

            preview here preview

            contactForm.component.html

            ...

            ANSWER

            Answered 2020-Apr-07 at 12:59

            You need to create a separate form component. Please check: - Template-driven forms from - https://angular.io/guide/forms and using within https://angular.io/guide/reactive-forms - This articles will help you - https://coryrylan.com/blog/building-reusable-forms-in-angular and https://coryrylan.com/blog/angular-form-builder-and-validation-management

            After that in your main component, you will iterate by "information" data and in template will use something like this:

            Source https://stackoverflow.com/questions/61080296

            QUESTION

            Select multiple entries in Tkinter treeview without pressing ctrl key
            Asked 2019-Oct-18 at 14:51

            I am trying to select multiple entries from Tkinter treeview. I used selectmode = extended for the same(use ctrl+enter key). But as soon as I try to open new branch in the tree(ctrl pressed), I am not able to open and if I do the same without pressing ctrl my selections from branch 1 disappears.

            Hence, I am trying to get some other way for selecting multiple nodes from Tkinter tree (from different brances) without pressing ctrl key. (i.e either remembering my mouse selections or some checkbox or any other suggestion)

            • Here is a working code example which works for multiple selection in different branches using ctrl key but I need multiple selection for selecting nodes in different branches without pressing ctrl as using this I am not able to open new branch after selecting first one and if released nodes opens but choices disappears.

            code:

            ...

            ANSWER

            Answered 2019-Oct-18 at 14:51

            The first thing you need to do is to set selectmode to None:

            Source https://stackoverflow.com/questions/58446788

            QUESTION

            Print parent name for each selection when selected multiple nodes in Tkinter tree
            Asked 2019-Oct-17 at 13:25

            I want user to select multiple nodes from different branches of Tkinter Tree. So that I can do further process I should know the parent branch of each selection.

            • When I select just one node I am able to get the parent id by using code below.
            • When I select multiple nodes(pressing the ctrl key),I just get parent node of first selection

            How can I get the parent node of all selections done simultaneously?

            Here is my working code:

            ...

            ANSWER

            Answered 2019-Oct-17 at 13:25

            selection()

            Returns a tuple of selected items.

            (source) (emphasis mine)

            .selection() returns a tuple of all items selected in the Treeview. On the first line of the function, you are explicitly only selecting the first item:

            Source https://stackoverflow.com/questions/58432977

            QUESTION

            Java sort by desired String
            Asked 2019-Sep-18 at 22:43

            I am new to the idea of comparators and I am looking into ways to sort strings. In my code, below, I have made a list and sorted through it using the Collections.sort() method. Here is the code:

            ...

            ANSWER

            Answered 2019-Sep-18 at 22:24

            You can use the Boolean.compare method to check if the strings begin with "Bob":

            Source https://stackoverflow.com/questions/58001346

            QUESTION

            Making two API calls with Retrofit to form one object
            Asked 2018-Aug-24 at 05:26

            I'm writing an app which makes unfortunately requires two API calls to complete one object. One call to TMDB to get a list of movies currently in theaters,and then another one to TMDB with the TMDB ID of each movie to get the IMDB ID.

            I might also later want to make a third call to OMDB to get the data from there as that's the data we're using on the movie page itself.

            I'm new to RXJava and fairly new to Retrofit. I did this the old fashioned way (well, I used OKHTTP) but i'd like to switch to a more elegant version with RXJava and this seems like the perfect use case to me.

            Sample First API Call

            ...

            ANSWER

            Answered 2018-Aug-24 at 02:45

            Do a combineLatest on the three network calls and wrap them in an object, then in subscribe pull the values out into your final object and send it to your presenter or display or other business logic

            Source https://stackoverflow.com/questions/51996635

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

            Vulnerabilities

            No vulnerabilities reported

            Install mavis

            The simplest way to use MAVIS is via Singularity. The MAVIS docker container used by singularity will take care of installing the aligner as well. Now you will run mavis via Snakemake as follows. For other installation options which do not use docker/singularity see the comprehensive install instructions in the user manual.

            Support

            All steps in the MAVIS pipeline are called following the main mavis entry point. The usage menu can be viewed by running without any arguments, or by giving the -h/--help option. Help sub-menus can be found by giving the pipeline step followed by no arguments or the -h options. Common problems and questions are addressed on the wiki. If you have a question or issue that is not answered there (or already a github issue) please submit a github issue to our github page or contact us by email at mavis@bcgsc.ca.
            Find more information at:

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            Install
          • PyPI

            pip install mavis

          • CLONE
          • HTTPS

            https://github.com/bcgsc/mavis.git

          • CLI

            gh repo clone bcgsc/mavis

          • sshUrl

            git@github.com:bcgsc/mavis.git

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