bonito | A PyTorch Basecaller for Oxford Nanopore Reads | Machine Learning library
kandi X-RAY | bonito Summary
kandi X-RAY | bonito Summary
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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Top functions reviewed by kandi - BETA
- 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
bonito Key Features
bonito Examples and Code Snippets
Community Discussions
Trending Discussions on bonito
QUESTION
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 04:18User 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.
QUESTION
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 20:58Seems 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:
QUESTION
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 10:49First 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,
QUESTION
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 12:56I 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:
QUESTION
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 15:38I 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!
QUESTION
This question is pretty weird. Say I have a file, called idiot.cpp, and it begins with:
...ANSWER
Answered 2020-Jun-02 at 22:04idiot.cpp
does not need to include anything included indirectly by idiot.h
to be able to compile.
The more interesting case: bonito.cpp
#include
s 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.
ExampleIf idiot.h
contains...
QUESTION
I'm trying to GET the following URL in Delphi using TIdHTTO
but it fails:
ANSWER
Answered 2020-May-13 at 18:43URLs 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:
QUESTION
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 09:37Use left join here
QUESTION
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 18:42You 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
QUESTION
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 22:09It 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.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install bonito
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.
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