pangolin | Software package for assigning SARS | Genomics library

 by   cov-lineages Python Version: v4.3 License: GPL-3.0

kandi X-RAY | pangolin Summary

kandi X-RAY | pangolin Summary

pangolin is a Python library typically used in Artificial Intelligence, Genomics applications. pangolin 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 download it from GitHub.

Phylogenetic Assignment of Named Global Outbreak LINeages. The pangolin web app is maintained by the Centre for Genomic Pathogen and Surveillance.
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            kandi-support Support

              pangolin has a low active ecosystem.
              It has 389 star(s) with 105 fork(s). There are 44 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 14 open issues and 354 have been closed. On average issues are closed in 33 days. There are 4 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of pangolin is v4.3

            kandi-Quality Quality

              pangolin has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              pangolin 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

              pangolin releases are available to install and integrate.
              Build file is available. You can build the component from source.
              It has 1023 lines of code, 65 functions and 16 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed pangolin and discovered the below as its top functions. This is intended to give you an instant insight into pangolin implemented functionality, and help decide if they suit your requirements.
            • Generate the final report
            • Append a note to the row
            • Expand a lineage alias
            • Adds relevant fields to the new row
            • Use pangoLEARN
            • Finds a reference sequence from a reference file
            • Clean a reference sequence from a reference sequence
            • Encodes a sequence into a single dataLine
            • Find the designation cache and alias file
            • Checks if the given query file is valid
            • Parse fastqc thresholds
            • Set up the analysis mode
            • Get all data files in a datadir
            • Print the version of a conda package
            • Emit a record
            • Print out the version of the installed tools
            • Install Pangolin - Assigns
            • Check all dependencies
            • Find the query fasta file
            • Runs auto - update
            • Create a dictionary with default configuration
            • Format a text message
            • Check for assignment cache file
            • Configure the logger
            • Set up the constellations
            • Set up a temporary directory
            Get all kandi verified functions for this library.

            pangolin Key Features

            No Key Features are available at this moment for pangolin.

            pangolin Examples and Code Snippets

            No Code Snippets are available at this moment for pangolin.

            Community Discussions

            QUESTION

            How to make confidence intervals "run off" the edge of a forestplot in R, so that other plots retain detail?
            Asked 2022-Mar-02 at 21:57

            I am visualizing a bunch of effects on different species in a forestplot using the R package jtools. One model has huuuuge confidence intervals compared to the rest, so I end up losing detail on the effect sized for other models(see image below).

            As you can see, the elephant CI is blowing out the graph to a different scale and the effect sizes for other species are hard to discern.

            Here is my code:

            ...

            ANSWER

            Answered 2022-Mar-02 at 21:57

            jtools::plot_summs returns a ggplot object, so it can be easily adjusted

            Source https://stackoverflow.com/questions/71329520

            QUESTION

            Pymongo vs pyscopg3: orders of magnitude difference for writes?
            Asked 2022-Feb-20 at 18:18

            I have an application that collects crypto prices from decentralized exchanges (nothing commercial, the goal is mainly to learn some databases techs with real data). I got it working with MongoDB and PostgresSQL. However, I'm seeing massive differences when it comes to writes, in favour of MongoDB. I'm talking several orders of magnitude. I know MongoDB is a NoSQL db and is advertised to be more efficient for this kind of stuff, but I was wondering if I'm missing something with my postgres implementation. I'll describe below how I implemented the logic and I'll try to provide comparable metrics (as much as I can).

            To talk to the databases, I use psycopg3 for the Postgres implementation, and pymongo for the MongoDB one.

            Here is the data structure I'm writing to the databases:

            ...

            ANSWER

            Answered 2022-Feb-20 at 18:18

            For batch import of data into Postgres generally the fastest way is to use the Postgres command COPY. In psycopg3 this is available via the procedures shown here psycopg3 COPY. The caveat is that COPY is all or none, either all the data is imported or an error means none of it is imported.

            Source https://stackoverflow.com/questions/71195034

            QUESTION

            Concatenating DataFrames and offsetting integer indices
            Asked 2021-May-07 at 10:54

            I've a dict of DataFrames I've retrieved and I want to concatenate them together into one large DataFrame. Each DataFrame was retrieved successively, and each has an index column which is an integer index from 0 to n-1. Each dataframe has at most n dataframes.

            ...

            ANSWER

            Answered 2021-May-07 at 10:54

            How about reseting the index

            Source https://stackoverflow.com/questions/67433532

            QUESTION

            Undefined Reference While Compiling ROS ORB_SLAM2
            Asked 2021-Apr-22 at 14:53

            I am trying to compile this version of ORB SLAM2 and after fixing some library import errors, I got this:

            ...

            ANSWER

            Answered 2021-Apr-22 at 14:53

            This is an annoying compatibility error. The ORB SLAM you are trying to use only works with Ubuntu 18.04. But, on the ROS ORB SLAM page, they have a new one called orb_slam_ros (click here) that does the same thing.

            NOTE: The new one doesn't say that it outputs ROS maps but using Octomap, you can convert a PointCloud to a Map. NOTE: This is tested in Ubuntu 20.04 ROS Noetic. As of now, 20.10 doesn't work.

            Source https://stackoverflow.com/questions/66198275

            QUESTION

            creating slider bar using pangolin
            Asked 2021-Feb-03 at 15:27

            Is there any way to create slider using pangolin? small example of creating slider with min and max value, when user clicks on ok button then call a function.

            ...

            ANSWER

            Answered 2021-Feb-03 at 15:12

            With some back Rand D i figured out a way to create a slider sort of thing: posting my answer incase if it can be of any ones help:

            Source https://stackoverflow.com/questions/66022458

            QUESTION

            cv2 triangulatePoints always returns same Z value
            Asked 2020-Oct-11 at 11:27

            I am trying to get 3D points using cv2.triangulatePoints but it always returns almost same Z value. My output looks like this: As it seen, all points are in almost same Z value. There is no depth.

            Here is my triangulation:

            ...

            ANSWER

            Answered 2020-Oct-10 at 15:03

            Ciao,

            unfortunately I don't have the possibility to double-check directly but my gut feeling is that the issues you are facing are essentially due to the choice of your first projection matrix

            I did some research and I found this great paper with both theory and practice. Despite differing a little bit from your approach, there is a thing that is worth saying

            If you check carefully, the first projection matrix is exactly the camera matrix with an additional last column equal to zero. In fact, the rotation matrix for the first camera reduces to the identity matrix and the corresponding translation vector is a null vector, so using this general formula:

            Source https://stackoverflow.com/questions/64260851

            QUESTION

            Open menu when it clicked
            Asked 2020-Oct-06 at 08:46

            In my website, I have a menu open when users click to toggle. It works fine when I click a link that moves to a particular section. What I want is when the user clicks a link close menu and view toggle. I able to do that but I can't open the menu again by clicking toggle again. Here is what done. When I click to toggle it is not view my menu.

            ...

            ANSWER

            Answered 2020-Oct-06 at 08:24

            You basically want the links clicked to replicate the behaviour of the hamburger menu click, why not just have it perform the same action?

            Source https://stackoverflow.com/questions/64221844

            QUESTION

            PHP Site not working after renaming/adding new page
            Asked 2020-Jun-10 at 15:37

            On my site, I had an index.php with a navbar. Then, I needed to add another page, called second.php, and updated my navbar code accordingly (I have a nav.html file for the navbar, so that I can use JS to load it onto each page of the site). I also added the navbar code to the second.php. However, when I opened index.php, the link to second.php didn't appear.

            I tried restarting my computer, restarting my MAMP server, reopening my code editor, reopening the browser, but nothing worked. Then, I tried renaming my files (for both the purpose of testing and because I needed better file names) and updated all instances of the name of the files accordingly. But then this appeared:

            followed by a list of the files in my directory. In particular, the site wasn't displaying. Could someone please explain what's happening and how I can fix it?

            nav.html:

            ...

            ANSWER

            Answered 2020-Jun-10 at 15:37

            I'm not clear on what isn't working at this point, so I might as well share a working example I have locally. I'm accessing my site at http://localhost/so/, and going to that URL will load any index page I have. I have 3 files inside the /so directory:

            nav.html (I removed your tags because those already exist in the other files):

            Source https://stackoverflow.com/questions/62267549

            QUESTION

            cv::namedWindow() crashed, Segmentation Fault
            Asked 2020-May-19 at 08:42

            This is a stochastic problem. When I re-make my project, this problem is more likely to happen. I used gdb core dump analysis and found out that cv::namedWindow function may be the reason?

            This is main.cpp

            ...

            ANSWER

            Answered 2020-May-19 at 08:42

            You should not open a cv::namedWindow from a thread that isn't the main thread. It might work, but I wouldn't recommend it.

            Source https://stackoverflow.com/questions/61883059

            QUESTION

            Cannot compile Pangolin on QT Creator
            Asked 2020-Mar-11 at 11:36

            I am new to pangolin and trying to compile a 'hello world' code of pangolin on Qt Creator. I have run into this "undefined reference" issue while compiling it. My code is simple :

            ...

            ANSWER

            Answered 2020-Mar-10 at 16:53

            As /home/mavbot/Pangolin/build/src is not a default place to look for libraries, you have to inform the dynamic linker (ld.so) to look there.

            You can do this by:

            • either setting the environment variable LD_LIBRARY_PATH=/home/mavbot/Pangolin/build/src every time you run your program, or
            • compiling your program with a "runpath". This will instruct ld.so to look there first. The flag is as follows:

            Source https://stackoverflow.com/questions/60618161

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

            Vulnerabilities

            No vulnerabilities reported

            Install pangolin

            You can download it from GitHub.
            You can use pangolin 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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