OPAL | OPAL : Open-community Profiling Assessment tooL

 by   CAMI-challenge Python Version: v1.0.12 License: Apache-2.0

kandi X-RAY | OPAL Summary

kandi X-RAY | OPAL Summary

OPAL is a Python library. OPAL has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Taxonomic metagenome profilers predict the presence and relative abundance of microorganisms from shotgun sequence samples of DNA isolated directly from a microbial community. Over the past years, there has been an explosive growth of software and algorithms for this task, resulting in a need for more systematic comparisons of these methods based on relevant performance criteria. OPAL implements commonly used performance metrics, including those of the first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations.
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            kandi-support Support

              OPAL has a low active ecosystem.
              It has 21 star(s) with 6 fork(s). There are 16 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 5 open issues and 44 have been closed. On average issues are closed in 265 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of OPAL is v1.0.12

            kandi-Quality Quality

              OPAL has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              OPAL is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              OPAL releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed OPAL and discovered the below as its top functions. This is intended to give you an instant insight into OPAL implemented functionality, and help decide if they suit your requirements.
            • Generate the HTML for the metrics table .
            • Create the metrics table .
            • Make a unifrac input from another profile .
            • Make the unifrac input from the other .
            • Convert Pandas dataframe to Pandas DataFrame format .
            • Open a tsv file from a tsv file .
            • Plot all metrics for a given metrics .
            • Generate a radar axes .
            • Compute the metrics for each group .
            • Plotrarefaction curves .
            Get all kandi verified functions for this library.

            OPAL Key Features

            No Key Features are available at this moment for OPAL.

            OPAL Examples and Code Snippets

            User Guide,Running
            HTMLdot img1Lines of Code : 59dot img1License : Permissive (Apache-2.0)
            copy iconCopy
            usage: opal.py -g GOLD_STANDARD_FILE -o OUTPUT_DIR [-n] [-f FILTER] [-p]
                           [-l LABELS] [-t TIME] [-m MEMORY] [-d DESC] [-r RANKS]
                           [--metrics_plot_rel METRICS_PLOT_REL]
                           [--metrics_plot_abs METRICS_PLOT_ABS] [  
            Steps
            HTMLdot img2Lines of Code : 7dot img2License : Permissive (Apache-2.0)
            copy iconCopy
            sudo apt install python3-pip
            
            sudo add-apt-repository universe
            sudo apt update
            
            pip3 install numpy==1.16.4
            pip3 install cami-opal
            
            echo 'PATH=$PATH:${HOME}/.local/bin' >> ~/.bashrc
            source ~/.bashrc
              
            Developer Guide,More examples,Tests
            HTMLdot img3Lines of Code : 1dot img3License : Permissive (Apache-2.0)
            copy iconCopy
            tox
              

            Community Discussions

            QUESTION

            Compile an opalized Ruby gem to Node package
            Asked 2021-Dec-28 at 23:25

            It's not clear to me from the docs and guides whether the following is feasible with Opal:

            I've written a builder gem which implements an API to build an object tree which is then written to XML (or AIXM to be exact, an aeronautical format). There are currently runtime dependencies, but I could get rid of those.

            There's a guide on configuring gems for Opal, however, is it possible to use an opalized gem in a JavaScript project? Or convert it to a Node package?

            ...

            ANSWER

            Answered 2021-Dec-28 at 23:25

            We are currently in a process of designing a good NPM integration. But as of now, yes. You can build an Opal project to a .js (or .mjs) file and require it in the Node environment.

            One issue though: Opal does not behave well in the JS environment, as it defines globals, modifies prototypes, etc. - it may cause a mess, though most incompatibilities have been sorted out over the years (in any case, you may consider running Opal code in a WebWorker). The main issue here is that such a package will inadvertently include opal corelib - and you should take care to include it just once. So, your Opal part of the application should be compiled together, not split together into multiple packages. We will work on correcting that issue in the following months.

            As for interfacing Opal from JS, you should take a look at this: https://github.com/opal/opal/blob/master/docs/compiled_ruby.md#ruby-from-javascript

            Source https://stackoverflow.com/questions/70404748

            QUESTION

            key is of invalid type
            Asked 2021-Oct-21 at 19:17

            Background: I am trying to rewrite Step 1 in this guide in Go language.

            I have

            I am trying to use this key to verify the JWT token. Here is my code

            ...

            ANSWER

            Answered 2021-Oct-21 at 14:58

            I'm think you'll have to return a *rsa.PublicKey instead of []byte from the jwt.KeyFunc. This is a guess looking at your key string

            Instead of:

            Source https://stackoverflow.com/questions/69662259

            QUESTION

            Laravel DOMDocument : failed to open stream: Permission denied
            Asked 2021-Oct-19 at 19:30

            I'm trying to generate xml file in Laravel, I use DOMdocument but I got this error message when I try to save the file :

            ...

            ANSWER

            Answered 2021-Oct-19 at 19:02

            Seems you need to provide writeble path to save method, like $dom->save(storage_path('result.xml'))

            Source https://stackoverflow.com/questions/69636172

            QUESTION

            Local Jekyll Serve/Live Site discrepancy - "view on Gihtub" button missing
            Asked 2021-Aug-22 at 14:50

            It's really a small things, but something I can't get out of my mind.

            When running gh-pages locally with jekyll serve I get the "View on Github" button, but it's missing on the live page. Everything is up to date, and all files are the same both locally and live.

            _config.yml

            ...

            ANSWER

            Answered 2021-Aug-22 at 14:50

            I found the issue in the header.

            Source https://stackoverflow.com/questions/68793105

            QUESTION

            Why can't we replace the def of "many" with the code using <~> in Opal?
            Asked 2021-May-31 at 10:24

            I have an question about https://github.com/pyrocat101/opal/blob/master/opal.ml.

            At line 105, I replaced the definition of many with let rec many x = option [] (x <~> many x);;. Then, I got the following error message:

            Stack overflow during evaluation (looping recursion?).

            However, these two codes seem to be same. Why?

            I used OCaml version 4.12.0.

            ...

            ANSWER

            Answered 2021-May-31 at 10:24

            OCaml is an eager language. Thus in

            Source https://stackoverflow.com/questions/67765723

            QUESTION

            Sorting a 2D string array in c
            Asked 2021-May-28 at 04:45

            I am trying to sort this file that has this information below

            ...

            ANSWER

            Answered 2021-May-28 at 04:45

            Below part is problematic in some ways:

            Source https://stackoverflow.com/questions/67732772

            QUESTION

            MPI_alltoallw working and MPI_Ialltoallw failing
            Asked 2021-Apr-21 at 07:07

            I am trying to implement non-blocking communications in a large code. However, the code tends to fail for such cases. I have reproduced the error below. When running on one CPU, the code below works when switch is set to false but fails when switch is set to true.

            ...

            ANSWER

            Answered 2021-Apr-21 at 07:07

            The proposed program is currently broken when using Open MPI, see issue https://github.com/open-mpi/ompi/issues/8763. The current workaround is to use MPICH.

            Source https://stackoverflow.com/questions/66932156

            QUESTION

            Why is my for loop not pulling the correct data from my array of objects?
            Asked 2020-Dec-14 at 22:10

            I have successfully got my jQuery to load individual data from my array of objects but when I tried to add a jQuery click event to enable a toggle feature (that loads the image of the div into a bigger 'fullscreen' view) it only loads the very last array item's data.

            Sample of my array of objects I'm calling allPictures:

            ...

            ANSWER

            Answered 2020-Dec-14 at 07:52

            Try this one...I just your code copy and modify code..

            Source https://stackoverflow.com/questions/65284783

            QUESTION

            tidy select syntax for multiple variable
            Asked 2020-Dec-09 at 03:47

            I have been unable to find a good example of how to use across/c_across with tidy select syntax to select variables that contain multiple strings. I find str_detect works well, but it doesnt seem to work inside dplyr verbs? The first line of summarise works in the code, but am looking for correct syntax to find variables containing both substrings in second and third line:

            ...

            ANSWER

            Answered 2020-Dec-09 at 00:15

            You can use the matches tidyselect function. matches applies any arbitrary regular expression to select columns.

            Source https://stackoverflow.com/questions/65208818

            QUESTION

            Appending a key:value from one dictionary to another
            Asked 2020-Nov-21 at 06:55

            So i want to be able to make a multiple choice quiz program using dictionaries. I have one dictionary with all the questions as the key and the answer as a value and a second dictionary thats empty. I want to append all of the incorrect questions someone may have into the empty dictionary. i want to do this in order to allow users to retake the exam but only with the questions that they answered wrong. Yet i cannot find a way to append a key and value from one list to another without being specific.

            Here is my code below:

            ...

            ANSWER

            Answered 2020-Nov-21 at 06:55

            Interesting problem to solve. Look at this code and see if it provides you the repeatable process to keep continuing with your quiz. The only area that I have a bit of a problem is your big if statements that check for scores and print varying responses. When the user has fewer questions, I had to add the older answered questions to the tally to stay in the same range. Otherwise, this should work.

            Things I changed.

            #1: Questions is a list of tuples. Each tuple is a question and answer (q1,'c') as example.

            #2: Since we need to repeat the questions, I am iterating through incorrect question list each time. To start off, I set all questions as incorrect. So the incorrect questions list has values 0 thru 14.

            #3: Every time the user answers correctly, I am removing the question from the incorrect question list.

            #4: Since I am manipulating the list itself by removing the correctly answered question, I cannot use a for loop. Instead I am using a while loop and ensuring I am going through the list only till the max of list

            #5: I am looping the Quiz function until the user decides to stop playing. To start with, I am setting the flag as yes and checking for it before I call Quiz function. I am returning the user's decision back as a return statement. That is helping the loop to keep going.

            #6: Finally, I moved all the questions outside and made Questions a global variable. Since we are going to call Quiz a few times, I didn't want Questions to be defined every time. If you want to keep it inside, its your choice. It does not impact the overall solution. However, you need to make it a list of tuples. Additionally, inc_questions has to be global so you can manipulate it as many times as you need.

            Below is the code. Let me know if you find any errors.

            Source https://stackoverflow.com/questions/64938506

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

            Vulnerabilities

            No vulnerabilities reported

            Install OPAL

            You can download it from GitHub.
            You can use OPAL 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

            Taxonomic metagenome profilers predict the presence and relative abundance of microorganisms from shotgun sequence samples of DNA isolated directly from a microbial community. Over the past years, there has been an explosive growth of software and algorithms for this task, resulting in a need for more systematic comparisons of these methods based on relevant performance criteria. OPAL implements commonly used performance metrics, including those of the first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations.
            Find more information at:

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            https://github.com/CAMI-challenge/OPAL.git

          • CLI

            gh repo clone CAMI-challenge/OPAL

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            git@github.com:CAMI-challenge/OPAL.git

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