SONIA | Infer selection pressures on features of amino acid CDR3 | Genomics library

 by   statbiophys Python Version: 0.2.2 License: GPL-3.0

kandi X-RAY | SONIA Summary

kandi X-RAY | SONIA Summary

SONIA is a Python library typically used in Artificial Intelligence, Genomics applications. SONIA 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 SONIA' or download it from GitHub, PyPI.

SONIA is a python 3.6/2.7 software developed to infer selection pressures on features of amino acid CDR3 sequences. The inference is based on maximizing the likelihood of observing a selected data sample given a representative pre-selected sample. This method was first used in Elhanati et al (2014) to study thymic selection. For this purpose, the pre-selected sample can be generated internally using the OLGA software package, but SONIA allows it also to be supplied externally, in the same way the data sample is provided. SONIA takes as input TCR CDR3 amino acid sequences, with or without per sequence lists of possible V and J genes suspected to be used in the recombination process for this sequence. Its output is selection factors for each amino acid ,(relative) position , CDR3 length combinations, and also for each V and J gene choice. These selection factors can be used to calculate sequence level selection factors which indicate how more or less represented this sequence would be in the selected pool as compared to the the pre-selected pool. These in turn could be used to calculate the probability to observe any sequence after selection and sample from the selected repertoire.
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            kandi-support Support

              SONIA has a low active ecosystem.
              It has 10 star(s) with 6 fork(s). There are 2 watchers for this library.
              There were 3 major release(s) in the last 6 months.
              There are 0 open issues and 1 have been closed. On average issues are closed in 208 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of SONIA is 0.2.2

            kandi-Quality Quality

              SONIA has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              SONIA 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

              SONIA 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 SONIA and discovered the below as its top functions. This is intended to give you an instant insight into SONIA implemented functionality, and help decide if they suit your requirements.
            • Adds generated sequences
            • Compute marginal marginal likelihood
            • Compute the energy of sequences
            • Updates the model
            • Saves the model to a directory
            • Find features in a sequence
            • Compute the sequence energy of sequences
            • Save the model to a directory
            • Compute the sequence energy from sequences
            • Compute the potential energy for a sequence of sequences
            • Compute all pgenens for a sequence of sequences
            • Load the model
            • Load features and model
            • Compute the joint marginal likelihood for each genotype
            • Compute the D KL divergence of a sequence
            • Compute the entropy of a sequence
            • Compute all the pgenens
            • Plot the log bar plot
            • Plots the length of the coefficients for the given length
            • Add a list of all the features to the chain
            • Plot the model learning rate
            • Generate the VL plot
            • Infer selection of data
            • Perform inference
            • Calculates the weight for the model
            • Add features to the model
            • Plots the ratio of genotype frequencies
            • Generate nucleotide sequences for post - sampling
            Get all kandi verified functions for this library.

            SONIA Key Features

            No Key Features are available at this moment for SONIA.

            SONIA Examples and Code Snippets

            How can I use a value in a dataframe to look up an attribute
            Pythondot img1Lines of Code : 13dot img1License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            df2 = pd.merge(df, df_students,  left_on="Student1", right_on="Student")
            df3 = pd.merge(df2, df_students,  left_on="Student2", right_on="Student")
            df3['Sum'] = df3[['Score_x','Score_y']].sum(axis=1)
            df3['Years Elapsed'] = 2022 - df3[['Year
            For loop in function not doing what I want
            Pythondot img2Lines of Code : 10dot img2License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            def loop_dates():
                'Runs the interpolate function for all the dates for one curve'
                for dt in AllDate:  
                    data = importdata(location, dt, C, max_maturity = '30Y') 
                    fwdrate = interpolate(data, '1y', '1y')
                    dictio
            copy iconCopy
            df2 = df2.set_index('Date')
            
            df1['Exreturn'] = df1['Return'] - df2['Daily SONIA Rate']
            
            #       Date   Adj Close    Return  Exreturn
            # 2019-01-02  475.365143       NaN       NaN
            # 2019-01-03  468.232574 -0.015004 -0.719804
            # 2019-01-04  48
            Obtaining specific characters from dataframe column
            Pythondot img4Lines of Code : 35dot img4License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            df.maturity.str.rsplit(n=1).str[-1]
            
            0      1W
            1      2W
            2      1M
            3      2M
            4      3M
            5      4M
            6      5M
            7      6M
            8      7M
            9      8M
            10     9M
            11    10M
            12    11M
            13     1Y
            14    18M
            15     2Y
            16     3Y
            17     4Y
            18     5Y
            19     6Y
            20
            IndexError: list index out of range when if len(listx[i]) > n
            Pythondot img5Lines of Code : 21dot img5License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            liste1 = ['Jean', 'Maximilien', 'Brigitte', 'Sonia', 'Jean-Pierre', 'Sandra']
            
            moins6 = []
            plus6 = []
            i = 0 
            
            while i < len(liste1) : # here is your error
                
                if len(liste1[i]) > 6: 
                    moins6.append(liste1[i])
                    
               
            IndexError: list index out of range when if len(listx[i]) &gt; n
            Pythondot img6Lines of Code : 15dot img6License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            liste1 = ['Jean', 'Maximilien', 'Brigitte', 'Sonia', 'Jean-Pierre', 'Sandra']
            
            moins6 = []
            plus6 = []
            
            for word in liste1:
                if len(word) > 6:
                    moins6.append(word)
                else: plus6.append(word)
            print(moins6)
            print(plus6)
            
            python function to reduce logical operators and operands in a list
            Pythondot img7Lines of Code : 23dot img7License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            2.  
            
                while 'and' in op:
                        j = op.index(7)
                        print("index", j)
                        # print(lovop)
                        fn(j, lovop)
                        op.pop(j)
                        print(lovop)
            
            def fn(ind,lsts):
                lsts[i
            Pandas:Dataframe issue
            Pythondot img8Lines of Code : 72dot img8License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
                In [58]: s = pd.Series({'a1': [['5261', '5247', '5246'], ['521', '5547', '5246']], 'f1': [['526', '557', '5246']], 'a0': [['1', '32', '26'], ['61', '47', '246']]})                                                
            
                In [59]: s        
            How to print "key" value of a list of key:value pairs?
            Pythondot img9Lines of Code : 8dot img9License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            for first, second in NetworkCommands:
                print('The first element is', first)
                print('The second element is ', second)
            
            for i in NetworkCommands:
                print('The first element is', i[0])
                print('The second ele
            Removal of List from Pandas DataFrame
            Pythondot img10Lines of Code : 22dot img10License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            >>> df = pd.DataFrame({
            ...     "ProArticle": ["a", "b", "c", "d"],
            ...     "Vector": [[0, 0], [1, 1], [2, 2], [3, 3]]
            ... })
            >>> vs = np.vstack(df.Vector)
            >>> vs
            array([[0, 0],
                   [1, 1],
                   [2, 2],
                

            Community Discussions

            QUESTION

            Move 2nd level sub-array to the top of the 1st level multidimentional array based on value of the sub-array
            Asked 2021-Jun-14 at 21:35

            I'm looping through a multidimensional array and am left with some values.

            This is the complete PHP code.

            ...

            ANSWER

            Answered 2021-Jun-09 at 18:41

            This will reorder $array2 (into a new variable $final). First it assembles a simple array $people of the names, then it reassembles $array2 by prioritizing based on the $people array. Was this what you wanted to accomplish?

            Source https://stackoverflow.com/questions/67909656

            QUESTION

            How to display data from .txt file using JavaFX GUI Application
            Asked 2021-May-12 at 00:50

            I would like to display a data from .txt report file using JavaFX. In my code, I'm trying to use Labels and Vbox to display the info in multiple formats in a GUI to scene. However, I'm having terrible outputting my results as GUI instead of the console. I tried to research my issue but I couldn't find the piece of info that I need to solve the problem.

            This is the report I need to display as a GUI Application using JavaFX:

            This is what my code displays as a GUI:

            Here is my source code:

            ...

            ANSWER

            Answered 2021-May-12 at 00:50

            I think you could use a combination of TableView and Pagination like it is described in this posting: JavaFX TableView Paginator

            Here is an example:

            App.java:

            Source https://stackoverflow.com/questions/67494536

            QUESTION

            Sort the list of cars and display them sort by make using Java?
            Asked 2021-Apr-30 at 13:13

            I have a question that sorts data from a car report of txt file.

            The question is: How do I listed cars sorted by their MAKE (Ford, Chevy ..etc). They only need the MAKE to be sorted so they can be all FORD cars under each other, then Chevy, DODGE .. so on and so forth like this:

            And this is what I have so far:

            Here's my source code:

            ...

            ANSWER

            Answered 2021-Apr-30 at 13:13

            it's pretty straightforward :

            1. read all element and put them in a list:

            Source https://stackoverflow.com/questions/67333238

            QUESTION

            how to read/list 30 lines per page in a large text file report in Java?
            Asked 2021-Apr-29 at 12:44

            I have a Java question that deals with reading the txt file and pulling data from it.

            It's a bunch of used cars stored in a txt report file. They have several different lots that they sell from. The lots are identified by the 5 digit zip code followed by a zip code extension at the beginning of each record. They would like a report that lists all cars sold from all lots. This is what I come up with:

            They would like the report to list 30 cars per page, on the report. Each page is to have headings and a page number. Like this:

            My question is how do I list 30 cars per page instead of all together (Each page 30 cars with headings and page #)?

            Here's my source code:

            ...

            ANSWER

            Answered 2021-Apr-29 at 12:44

            As I already stated in my comment you'd need to count the cars you've already processed and print new page headers when you've hit a multiple of 30 cars.

            First I'd suggest moving your header print statements to a separate method, e.g. printPageHeader(int pageNumber). Then change your loop like this:

            Source https://stackoverflow.com/questions/67315215

            QUESTION

            How to pass a property from an array to each of it nested child array with lodash?
            Asked 2021-Apr-20 at 16:18

            Hello let's take this example :

            ...

            ANSWER

            Answered 2021-Apr-20 at 16:18

            When it comes to performance, I always find that vanilla JS is faster than any library implementation. So I always prefer vanilla JS for this reason. Here, a non-lodash.js solution, that places the desired values into the array, though you can simply deep-clone your original array:

            Source https://stackoverflow.com/questions/67182394

            QUESTION

            For loop in function not doing what I want
            Asked 2021-Apr-13 at 16:51

            I have this loop:

            ...

            ANSWER

            Answered 2021-Apr-13 at 16:51

            I managed to solve the issue, I took dictionary = {dt:fwdrate} and fwdsdic.update(dictionary) out of interpolate and put it outside, so now my final function is:

            Source https://stackoverflow.com/questions/67060842

            QUESTION

            Why do I keep getting 'Nan' values when I try to add a column from a csv dataframe to an existing dataframe both opened on pandas?
            Asked 2021-Apr-04 at 02:06

            I have an existing dataframe (df1) in the format below:

            ...

            ANSWER

            Answered 2021-Apr-04 at 00:12

            It looks like your indexes are different. df1 seems to have Date as its index but df2 has Date as a column.

            Set df2's index to Date and you should be able to create the column as expected:

            Source https://stackoverflow.com/questions/66936806

            QUESTION

            Obtaining specific characters from dataframe column
            Asked 2021-Mar-04 at 17:39

            I have a dataframe:

            ...

            ANSWER

            Answered 2021-Mar-04 at 17:30

            would this fit your need?

            Source https://stackoverflow.com/questions/66479958

            QUESTION

            BigQuery SQL : Left Join with aggregate conditions
            Asked 2021-Feb-07 at 18:57

            I have two Tables like : Table1:

            ...

            ANSWER

            Answered 2021-Feb-07 at 18:03

            QUESTION

            Having common function for multiple struct
            Asked 2021-Jan-14 at 16:34

            I have a use case to define a function ( in example it is "Process") which is common for two struct (Bellow example: StudentStats and EmployeeStats) and for each struct, it has its own implementation for "Pending" function.

            When I run the example i get following error :

            ...

            ANSWER

            Answered 2021-Jan-14 at 16:34

            The problem is that your stats type embed the Stats struct:

            Source https://stackoverflow.com/questions/65722416

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

            Vulnerabilities

            No vulnerabilities reported

            Install SONIA

            SONIA is a python 2.7/3.6 software. It is available on PyPI and can be downloaded and installed through pip:.

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