bonito | A PyTorch Basecaller for Oxford Nanopore Reads | Machine Learning library

 by   nanoporetech Python Version: v0.7.1 License: Non-SPDX

kandi X-RAY | bonito Summary

kandi X-RAY | bonito Summary

bonito is a Python library typically used in Artificial Intelligence, Machine Learning, Pytorch applications. bonito has no bugs, it has no vulnerabilities, it has build file available and it has low support. However bonito has a Non-SPDX License. You can install using 'pip install bonito' or download it from GitHub, PyPI.

A PyTorch Basecaller for Oxford Nanopore Reads. Bonito supports writing aligned/unaligned {fastq, sam, bam, cram}. Bonito will download and cache the basecalling model automatically on first use but all models can be downloaded with -. The default ont-bonito package is built against CUDA 10.2 however CUDA 11.1 and 11.3 builds are available.
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            kandi-support Support

              bonito has a low active ecosystem.
              It has 337 star(s) with 101 fork(s). There are 33 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 69 open issues and 220 have been closed. On average issues are closed in 478 days. There are 3 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of bonito is v0.7.1

            kandi-Quality Quality

              bonito has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              bonito 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

              bonito 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 not available. Examples and code snippets are available.
              bonito saves you 967 person hours of effort in developing the same functionality from scratch.
              It has 3001 lines of code, 233 functions and 27 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed bonito and discovered the below as its top functions. This is intended to give you an instant insight into bonito implemented functionality, and help decide if they suit your requirements.
            • Run Picard
            • Returns the indices of the typical indices
            • Set the columns
            • Append a row to the table
            • Run the analysis
            • Write a fastq file
            • Encode a sequence of moves
            • Return a summary row for duplex summary
            • Load a mod_bases model from mod_bases
            • Load a torch model
            • Return the appropriate Bioformat object
            • Extract meta data from a FASTA file
            • Load numpy and validation set
            • Return the indices of the typical indices
            • Process an itemmap from an iterator
            • Create an RNN layer
            • Read chunks from a read
            • Get all reads from a directory
            • A context manager for creating a null file
            • Convert a bonito model into a dictionary
            • Get all read groups in a directory
            • Fit the model to workdir
            • Download the file
            • Helper function to call mod_mods
            • Linear decay function
            • Call a single model
            • Load the model
            • Find follow - on
            Get all kandi verified functions for this library.

            bonito Key Features

            No Key Features are available at this moment for bonito.

            bonito Examples and Code Snippets

            No Code Snippets are available at this moment for bonito.

            Community Discussions

            QUESTION

            Items not following order in HTML
            Asked 2021-Jul-29 at 04:18

            So if you go to diartefloral.tech and use cellphone dimension in the "Sobre Nosotros" part of the menu the footer is overlapping an image, i dont know how to fix this. Thats like the most relevant code, I'm using bootstrap, i got the in the morning with the navbar overlapping the footer but i fixed it by adding the body{ padding-top:60px;}

            ...

            ANSWER

            Answered 2021-Jul-29 at 04:18

            User agents will always display items in the DOM order.

            You mean customize css properties. I see you are doing great in your live site, try to use images that sizes less than 1.5Mb, it slows rendering visuals.

            Source https://stackoverflow.com/questions/68568687

            QUESTION

            OpenCV imdecode returns none
            Asked 2021-Mar-10 at 21:07

            I'm trying to read an image from url.

            For this, I created the funcion below. For some url I input, it works exactly how I wish, but for others, it doesn't. In this cases the cv2.imread(img, cv2.IMREAD_COLOR) function returns none.

            My code:

            ...

            ANSWER

            Answered 2021-Mar-10 at 20:58

            Seems there is some issue reading the file with urllib but I didn't dig into.

            I tried with import urllib.request as ur instead of from urllib.request import Request, urlopen.

            This works for me:

            Source https://stackoverflow.com/questions/66572289

            QUESTION

            In which case round(a, 2) and f'{a:.2f}' will give a different result? Python
            Asked 2021-Mar-09 at 10:49

            I have the following task:

            George is going to have guests tonight and he decides to buy bonito, horse mackerel, and mussels. He goes to the fish market to buy a few kilos of each. You enter the prices of mackerel and sprat in USD in the console. You also enter the quantity of bonito, horse mackerel, and mussels in kg. How much money will George need to pay the bill if the prices at the fish market are:

            • bonito - 60% more expensive than mackerel
            • horse mackerel - 80% more expensive than sprat
            • mussels - 7.50 USD/kg

            Input:

            • First line: price of mackerel (float number)
            • Second line: price of sprat (float number)
            • Third line: quantity of bonito in kg (float number)
            • Fourth line: quantity of horse mackerel in kg (float number)
            • Fifth line: quantity of mussels in kg (integer)

            Output: Result. A float number rounded to the second decimal place.

            My code is:

            ...

            ANSWER

            Answered 2021-Mar-09 at 10:49

            First of all your question asks about a:.2f, but you wrote print(f'{total:.2}'), so I'm going to use .2f

            In the case where the number has trailing zeros,

            Source https://stackoverflow.com/questions/66544349

            QUESTION

            How can i use Word Sense Disambiguation with spanish?
            Asked 2020-Jun-16 at 12:56

            I'm doing an udemy course (All the examples in English) but the problem is always when i start using Spanish, always there is a lack of libraries or compatibilities. I downloaded from https://www.datos.gov.co/Ciencia-Tecnolog-a-e-Innovaci-n/LAS-WordNet-una-WordNet-para-el-espa-ol-obtenida-c/8z8d-85m7 the data in CSV, but i'm trying to execute the following code but crashes with NoneType error, because of the description of the context, does anyone has any idea about how to deal with it? Thank you

            ...

            ANSWER

            Answered 2020-Jun-16 at 12:56

            I looked at the source for the lesk function, and if it is not explicitly passed a synsets argument it creates one by calling wordnet.synsets(ambiguous_word), but it doesn't pass a language option or anything.

            If no synset is found for the word it just returns None hence the error you're getting. You can explicitly pass a synset like:

            Source https://stackoverflow.com/questions/62408832

            QUESTION

            EntityManager createNativeQuery returning wrong result set in Java Springboot
            Asked 2020-Jun-04 at 15:38

            I am stuck in this for half a day. My question may be scary with the image and JSon but my problem is not that difficult. I think I included all the information need for one to help. I have the following query

            ...

            ANSWER

            Answered 2020-Jun-04 at 15:38

            I was very fraightened by the bug I was having, because createNativeQuery was like a light in the end of the tunnel after struggling with the limitations of JpaRepository. After getting rid of nulls on the database column now the results are pretty much what I expect. I don't know why my union with nulls running directly on the database works and with createNativeQuery it produces strange results. The particular column I was having problem is "descricao", some table had null some have characters. I hope it can help others!

            Source https://stackoverflow.com/questions/62158979

            QUESTION

            What am I able to (not) include in a .cpp file?
            Asked 2020-Jun-02 at 22:04

            This question is pretty weird. Say I have a file, called idiot.cpp, and it begins with:

            ...

            ANSWER

            Answered 2020-Jun-02 at 22:04

            idiot.cpp does not need to include anything included indirectly by idiot.h to be able to compile.

            The more interesting case: bonito.cpp #includes idiot.h and idiot.h includes x.h. If idiot.h only uses the content of x.h for private or anonymous namespace code - and bonito.cpp wants to use something from x.h too, then bonito.cpp should include x.h directly (redundantly).

            The justification is simple: idiot.h can't remove something from the public/protected interface without risking breaking client code, so if that happens then the clients have to expect to deal with it - possibly including an extra header too. BUT, the maintainer of idiot.h and idiot.cpp should be free to change private or anonymous namespace content within idiot.h without risking breaking client code, including which headers are included to support that private code.

            So, the inclusion is redundant at the time it's done, but that's done in the expectation that it might stop being redundant as idiot.h evolves.

            This best-practice model is not automatically enforced - you have to understand the way this should work and actively code to that model.

            Example

            If idiot.h contains...

            Source https://stackoverflow.com/questions/62140312

            QUESTION

            What special handling do we need if we are trying to execute GET in TIdHTTP with Chinese words as parameters
            Asked 2020-May-13 at 18:43

            I'm trying to GET the following URL in Delphi using TIdHTTO but it fails:

            ...

            ANSWER

            Answered 2020-May-13 at 18:43

            URLs do not allow non-ASCII characters (IRIs do, but those are not widely in use yet). In a URL, you must url-encode any non-ASCII characters (and other reserved) characters, such as with Indy's TIdURI class, eg:

            Source https://stackoverflow.com/questions/61781866

            QUESTION

            LARAVEL Getting 2 of the same columns
            Asked 2020-Apr-03 at 10:07

            I have a table that has animals and another that has the images of the animals (id_image, id_animal).

            The problem is that when I do this:

            ...

            ANSWER

            Answered 2020-Apr-03 at 09:37

            QUESTION

            AutoFilter all columns after every Search / Userform VBA
            Asked 2020-Mar-13 at 18:42

            I have a workbook that every time it opens, clears the workbook from any filter that it has, which it works. But i want to implement so, every time a search is done, the filter that was applied on that workbook is cleared. It's giving me an error which i can't solve.

            I tried also doing If Sheets("Datos").AutoFilterMode then Sheets("Datos").AutoFilterMode = False but gives me another error.

            Further on this, every time the second if its activated, the textbox which should fill the number of total rows that are filtered by surname, does not show anything, but it does when it applies the first if, which is the user ID. (If its needed to be asked on another topic, just miss this paragraph)

            ...

            ANSWER

            Answered 2020-Mar-13 at 18:42

            You can't count the number of filtered rows with End(xlUp).Row. You need to use SpecialCells(xlCellTypeVisible).Cells.Count. I don't understand the problem with the filter as it works for me. Try

            Source https://stackoverflow.com/questions/60664426

            QUESTION

            Chloropeth map in R not working out, I think the problem is in merging the data
            Asked 2020-Jan-29 at 00:19

            I'm trying to do a chloropeth map following this guide: https://www.r-graph-gallery.com/327-chloropleth-map-from-geojson-with-ggplot2.html

            I mixed a bit of the tutorial with this answer(Chloropleth map with geojson and ggplot2), since I wasn't getting the result I expected. The cities were being filled with the same color, and it seemed as R wasn't understanding the data as numeric, and filled every city that had at least 1 user with the default color. (tried using as.numeric, didnt work either)

            I downloaded "users by city" data from my website from Google Analytics using

            ...

            ANSWER

            Answered 2020-Jan-28 at 22:09

            It looks like you have a couple relatively large values, while most are small. This causes 'skewing' of your color scale in a way that looks less interesting. Instead of graphing number of users, consider mapping based on a quantile .

            Here is an implementation of grouping into quantiles using cut2() from Hmisc. In this case, values are cut into 5 groups.

            Source https://stackoverflow.com/questions/59954168

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

            Vulnerabilities

            No vulnerabilities reported

            Install bonito

            You can install using 'pip install bonito' or download it from GitHub, PyPI.
            You can use bonito 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 .
            Find more information at:

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            gh repo clone nanoporetech/bonito

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            git@github.com:nanoporetech/bonito.git

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