pepper | PEPPER-Margin-DeepVariant | Genomics library

 by   kishwarshafin Python Version: r0.8 License: MIT

kandi X-RAY | pepper Summary

kandi X-RAY | pepper Summary

pepper is a Python library typically used in Artificial Intelligence, Genomics applications. pepper has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can install using 'pip install pepper' or download it from GitHub, PyPI.

PEPPER-Margin-DeepVariant
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            kandi-support Support

              pepper has a highly active ecosystem.
              It has 203 star(s) with 39 fork(s). There are 8 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 10 open issues and 169 have been closed. On average issues are closed in 69 days. There are no pull requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of pepper is r0.8

            kandi-Quality Quality

              pepper has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              pepper 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

              pepper 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 are available. Examples and code snippets are not available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed pepper and discovered the below as its top functions. This is intended to give you an instant insight into pepper implemented functionality, and help decide if they suit your requirements.
            • polish a BAM file
            • Call consensus function
            • Polishes the CPU setup
            • Get a list of file paths from a directory
            • Run small batch of small chunks
            • Calculates the number of occurrences of a given sequence
            • Find the confident positions in the alignment
            • Calculate aligner aligned sequences
            • Train models
            • Add polish options
            • Merge VCF records
            • Add command line arguments to the given parser
            • Set parameters based on options
            • Argument for training images
            • Generate a pileup file
            • Run CMake
            • Add test arguments to the given parser
            • Make train images
            • Predict using pytorch model
            • Generate images for each chromosome
            • Arguments for find candidates
            • Add command line arguments for make images
            • Arguments for run inference
            • Call variant calling
            • Add training arguments to the given parser
            • Generate image and save to file
            Get all kandi verified functions for this library.

            pepper Key Features

            No Key Features are available at this moment for pepper.

            pepper Examples and Code Snippets

            No Code Snippets are available at this moment for pepper.

            Community Discussions

            QUESTION

            Removing single word strings from a Dataframe and moving them to a csv
            Asked 2022-Mar-28 at 14:31

            I'm trying to remove single word strings from a dataframe (ou) and move it to another dataframe (removedSet and allowedSet), and then to a csv (names.csv and removed.csv). I am able to filter out specific strings, but I am having trouble removing single words from the dataframe I just made allowedSet.

            So I need to use the two dataframes I just made and check them for the single word strings. I want to append the single words to the dataframe with removed strings removedSet and remove the single words from the other dataframe with only full names allowedSet.

            This is my desired output COMPnames.csv:

            ...

            ANSWER

            Answered 2022-Mar-28 at 14:31

            IIUC, use a regex with word boundaries and groupby to save your files:

            Source https://stackoverflow.com/questions/71648051

            QUESTION

            Find the original strings from the results of str_extract_all
            Asked 2022-Mar-24 at 11:24

            I'm still young to coding and cannot figure out better functions or results to some tasks by myself very often. I have a question on tracking the original string after using str_extract_all for a specific pattern.

            Here is an example data called "fruit".

            index Fruit 1 apple 2 banana 3 strawberry 4 pineapple 5 bell pepper

            I used str_extract_all(fruit, "(.)\\1") to extract duplicated consonants, and get "pp", "rr", "pp", "ll", "pp".

            Also tracked the original string (of those extracted results) by str_subset(fruit, "(.)\\1"). Here's what I get.

            index fruit 1 apple 2 strawberry 3 pineapple 4 bell pepper

            However, I want to know where "each" extracted result is from. Therefore, using str_subset cannot capture those results which are from the same string. The following dataframe is what I expect to gain.

            index fruit pattern 1 apple pp 2 strawberry rr 3 pineapple pp 4 bell pepper ll 4 bell pepper pp

            I'm not sure if I explain my question clearly. Any feedbacks and ideas will be appreciate.

            ...

            ANSWER

            Answered 2022-Mar-24 at 11:24

            Your code already did what you want. You just need to create an extra column to store the output of str_extract_all, like the following:

            Since str_extract_all() returns a list, we'll need to unnest the list to become rows.

            The final line of the code is to create a consecutive index (since "banana" is gone, index 2 will also be gone).

            Source https://stackoverflow.com/questions/71599906

            QUESTION

            Having troubles wrapping text to align with image using only flex
            Asked 2022-Mar-19 at 08:21

            I am trying to wrap text under an image using flexbox only, i have tried almost everything i can come up with, using flex-grow, flex-basis, flex-shrink. I've put all of the text and image into their own seperate div classes but still that didn't seem to help. The image is aligned with the text but the text won't wrap, the only way i got the image to align with the text is by using "text-align" im not sure why or how text align moved an IMAGE but it did.

            ...

            ANSWER

            Answered 2022-Mar-19 at 08:21

            The text does not overlap image width, you have to set the width for the parent div separately from the image so that the text will have the same width

            Source https://stackoverflow.com/questions/71536360

            QUESTION

            Compare data between two csv files and count how many rows have the same data
            Asked 2022-Mar-15 at 19:16

            Let's say I have list of all OUs (AllOU.csv):

            ...

            ANSWER

            Answered 2022-Mar-15 at 19:16

            Read your file first and create a list of objects. [{CN:’Clark Kent’,OU:’news’,dc:’company’,dc:’com’},…{…}]

            Once you have created the list you can convert it to data frame and then apply all the grouping, sorting and other abilities of pandas.

            Now to achieve this, first read your file into a variable lets call var filedata=yourFileContents. Next split filedata. var lines = filedata.split(‘\n’) Now loop over each lines

            Source https://stackoverflow.com/questions/71487592

            QUESTION

            JavaScript user input variable
            Asked 2022-Feb-04 at 16:30

            n00b here!

            I have managed to assemble JavaScript code and I don't understand why is not working correct.

            The code is designed to calculate the difference between a given date and today's date. I guess my logic in the script is not correct as no error show in the console.

            Here is the code:

            ...

            ANSWER

            Answered 2022-Feb-03 at 23:26

            QUESTION

            What is wrong with my Filter and Map function as its not filtering the correct item inside my React Component?
            Asked 2022-Jan-24 at 00:01

            Here is are my menu items, and I want to filter only the Drinks in a drink Component, I am displaying both the 'Drinks' and 'Eat' under categories. And my goal is to only filter and extract the 'Drinks' as I am displaying the drinks on its own component.

            Here is my data:

            ...

            ANSWER

            Answered 2022-Jan-24 at 00:01

            MenuItems.filter((item) => "Drinks") return always true

            What you should be doing is comparing the category to drinks.

            MenuItems.filter((item) => item.category === "Drinks")

            Source https://stackoverflow.com/questions/70826930

            QUESTION

            Pepper Robot Tablet: Cannot show the specific webpage on Pepper Tablet
            Asked 2022-Jan-15 at 07:47

            I came across an issue is I noticed not all website link can be shown on the Pepper Tablet, is that right? for example, I want to show this link: "https://rt-webchatapp-v5.netlify.app/" which I developed for users to register, but on the tablet, it is always white screen. Can anyone explain it? how can I show above link on Pepper Tablet?

            Thanks in advance.

            this website is I developed for my research, I have been used for at least 6 months, I am hopeing I can use on Pepper robot directly.

            ...

            ANSWER

            Answered 2022-Jan-15 at 07:47

            The webview on Pepper's tablet is old. It uses Javascript 1.7 and might not support newest javascript features.

            Source https://stackoverflow.com/questions/70007398

            QUESTION

            How to properly insert mask into original image?
            Asked 2022-Jan-12 at 17:54

            My goal is to cover a face with circular noise (salt and pepper/black and white dots), however what I have managed to achieve is just rectangular noise.

            Using this image:

            I found the face coordinates (x,y,w,h) = [389, 127, 209, 209] And using this function added noise
            Like:

            ...

            ANSWER

            Answered 2022-Jan-12 at 16:13

            Bitwise opperations function on binary conditions turning "off" a pixel if it has a value of zero, and turning it "on" if the pixel has a value greater than zero.

            In your case the bitwise_or "removes" both the black background of the mask and the black points of the noise.

            I propose to do it like this:

            Source https://stackoverflow.com/questions/70677393

            QUESTION

            Refresh positions of all draw points after deleting or moving - Matlab App designer
            Asked 2022-Jan-07 at 14:08

            I did an app designer GUI with two buttons and axes. The first one (LoadimageButton) is loading the pappers image and I can mark points until I press escape. The second button is printing out the point coordinates (PositionButton).

            I have noticed that after pressing the two buttons I can move points in the axes and change their positions or delete them. The issue is that when I press the delete (in the context menu) I get this error after pressing the PositionButton:

            ...

            ANSWER

            Answered 2022-Jan-07 at 14:08

            You could add a check within the PositionButtonPushed function for whether or not each pointhandles element is valid, report on it if so or remove it if not

            Something like

            Source https://stackoverflow.com/questions/70589980

            QUESTION

            How to output only relevant changes while scraping for new discounts?
            Asked 2021-Dec-13 at 21:32

            In a previous question I got the answer from Hedgehog! (How to check for new discounts and send to telegram if changes detected?)

            But another question is, how can I get only the new (products) items in the output and not all the text what is changed. My feeling is that the output I got is literally anything what is changed on the website and not only the new added discount.

            Here is the code, and see the attachment what the output is. Thanks again for all the effort.

            ...

            ANSWER

            Answered 2021-Dec-13 at 10:14
            What happens?

            As discussed, your assumptions are going in the right direction, all the changes identified by the difflib will be displayed.

            It may be possible to adjust the content of difflib but I am sure that difflib is not absolutely necessary for this task.

            How to fix?

            First step is to upgrade get_discounts(soup) to not only check if discount is in range but also get information of the item itself, if you like to display or operate on later:

            Source https://stackoverflow.com/questions/70316762

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

            Vulnerabilities

            No vulnerabilities reported

            Install pepper

            Please follow the quickstart guides to assess your setup. Please follow case-study documentations for detailed instructions.
            Docker: Oxford Nanopore variant calling quick start.
            Singularity: Oxford Nanopore variant calling quick start.

            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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