flair | Full-Length Alternative Isoform analysis of RNA | Genomics library

 by   BrooksLabUCSC Python Version: 1.7 License: Non-SPDX

kandi X-RAY | flair Summary

kandi X-RAY | flair Summary

flair is a Python library typically used in Artificial Intelligence, Genomics applications. flair has no bugs, it has no vulnerabilities and it has high support. However flair build file is not available and it has a Non-SPDX License. You can install using 'pip install flair' or download it from GitHub, PyPI.

FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
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            kandi-support Support

              flair has a highly active ecosystem.
              It has 154 star(s) with 70 fork(s). There are 15 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 29 open issues and 210 have been closed. On average issues are closed in 123 days. There are 1 open pull requests and 0 closed requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of flair is 1.7

            kandi-Quality Quality

              flair has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              flair has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              flair releases are available to install and integrate.
              Deployable package is available in PyPI.
              flair 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.
              flair saves you 2907 person hours of effort in developing the same functionality from scratch.
              It has 6280 lines of code, 156 functions and 44 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed flair and discovered the below as its top functions. This is intended to give you an instant insight into flair implemented functionality, and help decide if they suit your requirements.
            • Count the number of transcripts for a set of reads
            • Check if a transcript is stringent
            • Check if the splice is covered by the given position
            • Return True if two sequences are far far far
            • Find the best sites for a given chromosome
            • Edit BED12 line
            • Find the best sites for a splice junction chain
            • Edit a single transcript line
            • Convert from start to bed12 format
            • Binary search
            • Parse command line options
            • Write a list of models to a single file
            • Find altSS
            • Add other junction
            • Command line utility
            • Run Denseeq
            • Yield junctions for junctions
            • Argument parser
            • Parse flair - diff
            • Run DRIM
            • Runs se_collapse
            • Split counts matrix into isoformats
            • Run rundrimseq
            • Convert a gtf file to a dictionary
            • Command line options
            • Build a graph from isoform
            Get all kandi verified functions for this library.

            flair Key Features

            No Key Features are available at this moment for flair.

            flair Examples and Code Snippets

            No Code Snippets are available at this moment for flair.

            Community Discussions

            QUESTION

            PRAW Posting new submission with a flair?
            Asked 2022-Mar-21 at 13:29

            Trying to post to a subreddit that requires flairs

            ...

            ANSWER

            Answered 2022-Mar-21 at 13:29

            You can find the available flair ids with

            Source https://stackoverflow.com/questions/71549840

            QUESTION

            what does "in-memory" means ? In the context of hadoop
            Asked 2022-Mar-07 at 15:17

            I read this line

            when you are starting namenode, latest fsimage file is load into “in-memory”. and at the same time, edit log file is also loaded into memory if fsimage file doesn’t contain up-to date information

            from https://data-flair.training/forums/topic/in-which-location-namenode-stores-its-metadata-and-why/ they are using term "in-memory" and "memory" are they different ?

            ...

            ANSWER

            Answered 2022-Mar-07 at 15:17

            No they aren't different. They are loaded into RandomAccessFile if that helps to think about. For reference here is FSImage. To help you see how this is done.

            Source https://stackoverflow.com/questions/71370995

            QUESTION

            Why is union() a narrow transformation and intersection() is a wide transformation in spark?
            Asked 2022-Jan-09 at 16:44

            I am trying to understand the underlying concept in Spark from here. As far as I have understood, narrow transformation produce child RDDs that are transformed from a single parent RDD (might be multiple partitions of the same RDD). However, union and intersection both require two or more RDDs for the transformations to be performed. Can someone please clear this theoretically?

            ...

            ANSWER

            Answered 2022-Jan-09 at 16:40

            No, your understanding is incorrect. A a narrow transformation is the one that only requires a single partition from the source to compute all elements of one partition of the output. union is therefore a narrow transformation, because to create an output partition, you only need the single partition from the source data.

            Intersection on the other hand is wide, because even for a single partition of the output, it requires access to the entire content of (at least) one of the source rdds.

            Source https://stackoverflow.com/questions/70643086

            QUESTION

            How to predict actual future values after testing the trained LSTM model?
            Asked 2021-Dec-22 at 10:12

            I have trained my stock price prediction model by splitting the dataset into train & test. I have also tested the predictions by comparing the valid data with the predicted data, and the model works fine. But I want to predict actual future values.

            What do I need to change in my code below?

            How can I make predictions up to a specific date in the actual future?

            Code (in a Jupyter Notebook):

            (To run the code, please try it in a similar csv file you have, or install nsepy python library using command pip install nsepy)

            ...

            ANSWER

            Answered 2021-Dec-22 at 10:12

            Below is an example of how you could implement this approach for your model:

            Source https://stackoverflow.com/questions/70420155

            QUESTION

            Chi squared test for significance
            Asked 2021-Nov-19 at 03:46

            I want to report on the difference between males and female fish in migration tactics. Would this be a chi-squared test? This is my data:

            ...

            ANSWER

            Answered 2021-Nov-19 at 03:46

            Now we can create a table and compute Chi square:

            Source https://stackoverflow.com/questions/70028319

            QUESTION

            bsddb.btopen alternative on Google Colab?
            Asked 2021-Nov-09 at 12:50

            So I have my Notebook on Google Colab using Python 3 (and I will implement some Deep learning libraries ex: Keras, TF, Flair, OpenAI...) so I really want to keep using Python 3 and not switch to 2.

            However, I have a .db file that I want to open/read, the script is written in Python 2 because they are using bsddb library (which is deprecated and doesn't work on Python 3)

            ...

            ANSWER

            Answered 2021-Nov-09 at 12:50

            berkeleydb is only Python binding on database BerkeleyDB created in C/C++.

            When I try to install it on my local system Linux Mint then I see error with

            Source https://stackoverflow.com/questions/69897261

            QUESTION

            Convert dataframe for category percentages in python
            Asked 2021-Oct-03 at 18:22

            i would like to convert a dataframe with calculating percentage points for a graph later on in python.

            The current frame looks like this

            Post ID Title Url Author Score Submission_Date Total_Num_of_Comments Permalink Flair Selftext TitleAndText Word Count k4nllk Update: Whassup bro? https://www.reddit.com/r/GME/comments/k4nllk/update_whassup_bro/ matt_xndever 1 2021-01-01 16:58:48 13 /r/GME/comments/k4nllk/update_whassup_bro/ Hedge Fund Tears asdasdasd asdasdasdasd 59.0

            Where flairs are the categories i want to look for (over 40). On one submission day (i want to look onto days only), there can be multiple posts with different flairs. These flairs should add up to 100%.

            So i want to create a dataframe like that:

            Submission_Date Discussion Due Diligence Hedge Fund Tears News 01.01.2021 NaN NaN 1.0 NaN 03.01.2021 NaN 0.333333 0.666667 NaN

            My graph should look like this: Plot stacked (100%) bar chart for multiple categories on multiple dates in Python

            Can someone help me with the preparation for that?

            Thanks and best regards

            ...

            ANSWER

            Answered 2021-Oct-03 at 18:11

            You can approach the problem as follows:

            • iterate over unique dates and slice the dataframe for each date
            • compute counts for each flair category with pandas value_counts()
            • get shares by dividing over the size of each slice
            • transpose the pandas series containing the shares for appending
            • append the shares for each date

            Here is a sample input:

            Source https://stackoverflow.com/questions/69426942

            QUESTION

            How to apply Entity Framework migration scripts to restore a database in an existing ASP.NET Core Web application
            Asked 2021-Sep-21 at 19:54

            I have an existing ASP.NET Core Angular Web application with the usual flairs. It comes with set of migration scripts (e.g. 20151227555555_AddIdentity.cs, 20161227444444_AddCoreEntities.cs etc) in a Migration/ code folder, each has Up, Down, and BuildTargetModel methods.

            then there is another folder called MigrationScript that contains the equivalent of table creation SQL scripts (straight-up CREATE TABLE...) for the various database entities.

            I am used to running database management and recreation/restore via a database project that I can "publish". I am new to the EF Migration way of doing it, so how do I run those migration C# scripts to create the database?

            ...

            ANSWER

            Answered 2021-Sep-21 at 19:54

            The fact that the C# migration scripts already contains Up() and Down() methods means they are ready to be applied. (Note: usually the Up and Down methods are created by the Add-Migration migrationname command).

            Here is how to apply the C# entity framework migration scripts in an existing project:

            1. Create the empty database with the correct database name. The database name is usually defined in the aspsettings.json file under ConnectionStrings group. Open Microsoft SQL Server Management Studio, create an empty database with the correct name.

            2. In Visual Studio Solution Explorer, right-mouse click on the project that contains the Migration folder (where the C# migration scripts are located), choose Manage NuGet Packages... and look under Installed tab to see if Microsoft.EntityFrameWorkCore.Tools package is installed, if not go ahead install it. Because that is the package that contains the EF migration commands, i.e. Add-Migration, Update-Database etc

            3. With the Microsoft.EntityFrameWorkCore.Tools package installed in the project that contains the Migration folder, open the Package Manager Console via Tools -> NuGet Package Manager -> Package Manager Console menu options.

            4. At the Package Manager Console prompt, type the command Update-Database, then all of the migration scripts will be applied and the tables created in the local SQL Server database created in step 1.

            Source https://stackoverflow.com/questions/69273294

            QUESTION

            Why aren't these regular expressions not working with exclamation point?
            Asked 2021-Aug-26 at 01:51

            Background info: I have some code that should pull results from a subreddit whenever they have the flair "loot", look for codes in the format XXXX-XXXX-XXXX, XXXX-XXXX-XXXX-XXXX, or those two without dashes, and output the codes in the console to be copy-pasted in another window. I also have it output any erroneous codes at the bottom for manual input later. The code runs fine, but the output is not the way that I want it, as explained later.

            Currently, the code works perfectly with alphanumeric codes, but gives an error when an "!" is in the code. I have set the range to include !, so I do not know what is setting off the error. I also have the code over at https://www.mycompiler.io/view/EgXpTO0 , which can be run there to see what I see.

            ...

            ANSWER

            Answered 2021-Aug-25 at 20:46

            The reason your codes do not work when they end with an "!" is because \b indicates a position of a word boundary ((^\w|\w$|\W\w|\w\W)). ! is not a part of a word.

            To fix this, you can use something like: (^(?=[\w!])|(?<=[\w!])$|(?<=[^\w!])(?=[\w!])|(?<=[\w!])(?=[^\w!])) at the end.

            This regex is essentially \b, with ! included.

            Source https://stackoverflow.com/questions/68929212

            QUESTION

            How to generate _id pages for movies using NUXT generated from API fetched from the movie DB
            Asked 2021-Aug-13 at 14:30

            This is my folder structure:

            This is how page looks like:

            I have got all necessary data from props, but I fail to understand how to generate dynamic id pages. I want to generate dynamic ~/movies/_id pages, based on the id pulled from an array from API. And that pages just have to get Title, picture and overview from API object. So those two are questions.

            Movies.vue is parent page. movieComp is component I have used to v-for on, to display list of a movies received from the array from API. Below every movie picture is a details button that should lead to that movie details (based on the id received from API).

            _id.vue is a page that I want to display based on the id received from API.

            This is code in movies.vue (parent).

            ...

            ANSWER

            Answered 2021-Aug-13 at 14:30

            What you need is to create a movies subfolder in which you add _id.vue and movies.vue (renamed index.vue).

            You should have the folowing folder structure:

            Source https://stackoverflow.com/questions/68773230

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

            Vulnerabilities

            No vulnerabilities reported

            Install flair

            You can install using 'pip install flair' or download it from GitHub, PyPI.
            You can use flair 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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