OPAL | OPAL : Open-community Profiling Assessment tooL
kandi X-RAY | OPAL Summary
kandi X-RAY | OPAL Summary
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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Top functions reviewed by kandi - BETA
- 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 .
OPAL Key Features
OPAL Examples and Code Snippets
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] [
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
Community Discussions
Trending Discussions on OPAL
QUESTION
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 23:25We 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
QUESTION
Background: I am trying to rewrite Step 1 in this guide in Go language.
I have
- a JWT token (
tokenString
using RS256 algorithm which can be viewed here) - a key (
key
in SSH RFC-4253 format).
I am trying to use this key to verify the JWT token. Here is my code
...ANSWER
Answered 2021-Oct-21 at 14:58I'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:
QUESTION
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 19:02Seems you need to provide writeble path to save method, like
$dom->save(storage_path('result.xml'))
QUESTION
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 14:50I found the issue in the header.
QUESTION
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 10:24OCaml is an eager language. Thus in
QUESTION
I am trying to sort this file that has this information below
...ANSWER
Answered 2021-May-28 at 04:45Below part is problematic in some ways:
QUESTION
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 07:07The 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.
QUESTION
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 07:52Try this one...I just your code copy and modify code..
QUESTION
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 00:15You can use the matches
tidyselect function. matches
applies any arbitrary regular expression to select columns.
QUESTION
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 06:55Interesting 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.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install OPAL
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.
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