AMBER | AMBER : Assessment of Metagenome BinnERs
kandi X-RAY | AMBER Summary
kandi X-RAY | AMBER Summary
AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation.
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Top functions reviewed by kandi - BETA
- Plots the taxonomic results
- Plot histogram
- Plot the heat maps for the histogram
- Plot precision vs bin size
- Compute metrics for each sample
- Compute the random index from a confusion matrix
- Parses the file
- Delete missing keys
- Generate a boxplot for each sample
- Create a list of colors
- Test for the unifrac analysis
- Test for real data
- Returns a pandas dataframe of the metrics
- Saves computed metrics
- Plots the average precision recall
- Opens the coverage file
- Plot precision recall scores
- Compute metrics for each chromosome
- Plot precision coverage by coverage
- Plot a histogram of a genome
- Add column to mapping
- Get heatmap colors from pandas dataframe
- Generate genome binning plot
- Creates the taxonomic binning plot
- Create the HTML for the genome binning
- Plots the contamination plot
AMBER Key Features
AMBER Examples and Code Snippets
Lines of Code : 67License : Strong Copyleft (GPL-3.0)
Copyusage: AMBER [-h] -g GOLD_STANDARD_FILE [-l LABELS] [-p FILTER]
[-n MIN_LENGTH] -o OUTPUT_DIR [--stdout] [-d DESC] [--silent]
[-v] [-m] [-x MIN_COMPLETENESS] [-y MAX_CONTAMINATION] [-c]
[-r REMOVE_GENOMES] [-k K usage: add_length_column.py [-h] -g GOLD_STANDARD_FILE -f FASTA_FILE
Add length column _LENGTH to gold standard mapping and print mapping on the
standard output
optional arguments:
-h, --help show this help message and exit
-g GOLD_S usage: convert_fasta_bins_to_biobox_format.py [-h] [-o OUTPUT_FILE]
paths [paths ...]
Convert bins in FASTA files to CAMI tsv format
positional arguments:
paths FASTA files including f Community Discussions
Trending Discussions on AMBER
QUESTION
ANSWER
Answered 2021-Aug-29 at 22:29You set size.width to height of Container instead of size.height:
QUESTION
I'm trying to make a Bottom Navigation Bar in Flutter but it keeps showing a shadow in front of the Navigation Bar. The code below is the code that taken from the flutter websites which has guarantee 100% work. But the fact is I keep failing because it doesn't work well on my Flutter. Is the version/SDK the problem?
...ANSWER
Answered 2022-Mar-31 at 05:14Set elevation: 0.0, Inside your BottomNavigationBar widget
QUESTION
Hey guys I have the following array that's used to display a flatlist within my app.
...ANSWER
Answered 2022-Mar-30 at 09:04You could create an object with counts of selected subjects and sort descending by this value.
QUESTION
As the title above, I want the page I've scrolled down to scroll back up when the BottomNavigationBar is pressed (double-pressed). I've managed to make it, no problem. But there is a problem if on the page there is contain a TabBar.
For Example I have a bottom navigation bar, that contains two pages:
HomePage and ProfilePage
On the HomePage I have a TabBar, and that contains two pages also:
FirstTabBarView and SecondTabBarView
The problem is when I've scrolled those two pages down (HomePage & ProfilePage at a different) I just want the FirstTabBarView view page to scroll to the top if I'm currently opening the FirstTabBarView page. But from my code, if I press the BottomNavigationBar button twice, both FirstTabBarView and SecondTabBarView both scroll up.
This is just a simple code sample, you can copy-paste and test it on the dart pad directly
...ANSWER
Answered 2022-Mar-29 at 04:27You will have to lift up the TabController along with the scrollcontrollers. Then use the TabController's index getter to check which tab is currently open.
QUESTION
I am using Tailwind CSS for my Laravel application, and want to remove the focus border on the input boxes. According to the documentation, focus:outline-none should achieve this, although it is not working for me and the border still appears on focus.
It looks like I am targeting the wrong thing, as if I do focus:outline-black, I can see a black outline as well as the standard blue one on focus.
focus:border-none also does not fix the problem.
Any ideas?
...ANSWER
Answered 2021-Nov-16 at 02:25Maybe you can try add focus:outline-none direct in your class.
QUESTION
I am trying to add a boxShadow to a Container but the BoxShadow is spreading over full width of screen instead of width of Sized Box. For futher explanation Container is a child of a SizedBox and SizedBox is in Column the crossAxisAlignment of the Column is stretch. The code is given below.
ANSWER
Answered 2022-Mar-25 at 12:04This is occur because of crossAxisAlignment value, using CrossAxisAlignment.stretch will stretches children across the cross axis.
the docs says "If a child wants a different size from its parent and the parent doesn’t have enough information to align it, then the child’s size might be ignored. Be specific when defining alignment."
To fix this you can either use other crossAxisAlignment value and provide the device width to the parent Container
QUESTION
I was dealing with the ScaffoldMessenger.of(context).showMaterialBanner method and it needs a MaterialBanner widget as parameter.
In my case I need to put an empty MaterialBanner widget but with a custom height (less than default).
In few words override the original MaterialBanner build method.
What I triedso I thought that I had to extend a StatefulWidget implementing MaterialBanner:
...ANSWER
Answered 2022-Mar-04 at 12:00The main issue was the return type of the "withAnimation" method. It has to be the same type of your custom widget. So:
QUESTION
in my nuxt app , after changing route using this.$router.push({ path: '/path' }) i got the nodeOps.tagName(...) is undefined in firefox , in chrome i get cannot get access to .toLowerCase() of undefined in the same line .
it happens in createPatchFunction of vue.runtime.esm.js versions: nuxt:^2.14.12, vue:^2.6.12
ANSWER
Answered 2021-Aug-25 at 12:24It looks like you have an older version of Node? https://github.com/nuxt/nuxt.js/issues/2385#issuecomment-358111543
Try to upgrade it to the latest LTS aka 14 and double-check that you got the latest version of Nuxt too.
QUESTION
I have two datasets: one includes customer's family details and another one includes classes associated with those customers. I would like to replace the name of customers with IDs for privacy reasons. An example of data is
dataset 1 (customer's family relationships)
...ANSWER
Answered 2022-Mar-01 at 23:46I think this should work, you can create a dictionary to asign unique identification numbers for each customers and then, in whatever dataframe you need, you just pull that customers id.
QUESTION
I am facing some issues with loading images from URLs in Flutter. Here is my code:
...ANSWER
Answered 2022-Feb-21 at 12:27Yes, you are correct with the implementation. So the thing is, NetworkImage tries to load the image and fails to load it. And hence, the _loadAsync() method rethrows the exception. Now, as you have provided errorBuilder, the framework uses that widget to show when an exception occurs. Hence, you are getting an exception that is rethrown from the framework but is handled as you have provided errorBuilder. Now, if you remove the errorBuilder you will get the exception logged in debug console, as well as the user, will be able to see that red exception screen if in debug mode and grey screen in release mode.
So, you are correct with the implementation as well as your doubt, but you missed the exact explanation of errorBuilder.
I hope this made your doubt clear!
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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No vulnerabilities reported
Install AMBER
You can use AMBER 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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