mavis | Merging , Annotation , Validation , and Illustration | Genomics library
kandi X-RAY | mavis Summary
kandi X-RAY | mavis Summary
MAVIS is python command-line tool for the post-processing of structural variant calls. The general MAVIS pipeline consists of six main stages.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- 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
mavis Key Features
mavis Examples and Code Snippets
pip install -U setuptools pip
pip install mavis_config # also installs snakemake
snakemake \
-j \
--configfile \
--use-singularity \
-s Snakefile
Community Discussions
Trending Discussions on mavis
QUESTION
dispatcher-servlet.xml
...ANSWER
Answered 2021-Jun-14 at 02:53This issue is solved after correcting up my code
QUESTION
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 00:28Looks 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.
QUESTION
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 20:30As 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
QUESTION
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 06:19Here is how you can proceed.
Let's assume you want to fetch stationName
from stations
array,
QUESTION
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 13:25If you want to identify the missing relationships you can do something like this:
QUESTION
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 12:59You 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:
QUESTION
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 14:51The first thing you need to do is to set selectmode
to None:
QUESTION
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 13:25selection()
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:
QUESTION
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 22:24You can use the Boolean.compare
method to check if the strings begin with "Bob":
QUESTION
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 02:45Do 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
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install mavis
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page