dark-matter | Python tools for filtering and visualizing Next Generation | Genomics library
kandi X-RAY | dark-matter Summary
kandi X-RAY | dark-matter Summary
A collection of Python tools for filtering and visualizing Next Generation Sequencing reads. Runs under Python 2.7 (mostly), 3.5, 3.6, and 3.7. Change log.
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Top functions reviewed by kandi - BETA
- Write the pathogen data to a HTML file
- Compute unique read counts
- Render the help page
- Make a sort function for samples
- Make an HTML table of reads
- Return an explanation of the given sequence identity
- Compute the identity between two reads
- Checks if two ids are equal
- Adds FASTA filtering options to an argparse parser
- Summarize the genome
- Retrieve consensus from a BAM file
- Format a DNAMatch object into a string
- Create an argument parser
- Compare two reads
- Generate an alignment panel of titles
- Run a command
- Split a FASTA file into a list of readors
- Add FASTA editing command line options
- Add a new FASTA file
- Determine whether this sequence should be filtered
- Create a bowtie2
- Compare two DNA sequences
- Normalize HSP
- Filters reads based on readAlignments
- Add a file to the dataset
- Plots the alignment of titles
dark-matter Key Features
dark-matter Examples and Code Snippets
Community Discussions
Trending Discussions on dark-matter
QUESTION
The TypeScript team has been doing great work on string literal typing in recent updates (4.1 & 4.2). I am wondering if there is a way to type a fixed length string.
Ex.
...ANSWER
Answered 2021-Feb-15 at 17:49There is no way to represent fixed-length strings with Typescript. There is a very upvoted proposal here, but still this feature has not been released.
If the length is very little, there are some workarounds suchs as the following:
QUESTION
I am facing a problem with two existing gradle projects that worked fine a couple of months ago but that show now an annoying error in the buildSrc folder, where I use the org.gradle.api.JavaVersion constant.
The project compiles correctly and is imported to IntelliJ. I can also run it so I guess everything is working but of course I don't like to get an error thrown into my face ;)
Here are both example projects:
They are both a multi-project with a core, desktop and android project. In both projects I use a buildSrc folder to define the versions in a common place for the entire project.
For whatever reason, IntelliJ is now showing an error "unresolved reference JavaVersion" in the Dependencies.kt/versions.kt file.
The build.gradle.kts of the buildSrc folder looks like this:
...ANSWER
Answered 2020-Nov-13 at 11:10This is an Intellij IDEA 2020.2 bug: https://youtrack.jetbrains.com/issue/KT-40683. Dependencies are unresolved in the buildSrc module, when you also have an Android module in the project.
As a possible workaround, please use IDEA 2020.1.
QUESTION
In my Azure DevOps Pipeline
(https://dev.azure.com/TheNewThinkTank/dark-matter-attractor/_build?definitionId=2&_a=summary)
I have a test stage from where I wish to install and run pytest on all Python files in the corresponding Azure DevOps repository
(https://dev.azure.com/TheNewThinkTank/_git/dark-matter-attractor).
The way Pytest is installed and run follows the official Microsoft documentation:
...ANSWER
Answered 2020-Oct-25 at 21:31Please try python -m pytest:
QUESTION
As the first step to my Azure DevOps pipeline I wish to validate my Python files by running pylint. This causes the pipeline to fail. My project is publicly available under this address:
https://dev.azure.com/gcr84/dark-matter-attractor
where all code is visible in the repo, and a pipeline run history is available. I would like to learn why the pylinting causes the pipeline to fail, and I have tried to add the command:
"|| pylint-exit $?"
(see https://pypi.org/project/pylint-exit/),
as well as
failOnStderr: false
(see https://docs.microsoft.com/en-us/azure/devops/pipelines/tasks/utility/bash?view=azure-devops).
Below is my bash command:
...ANSWER
Answered 2020-May-14 at 10:05After check you logs, this seems to be an expect behavior which not related to Azure DevOps side.
QUESTION
I have a map application with custom interactive layers, but I want to use the dark theme from this. I'm using playing around on jsfiddle and I just can't seen to get the dark theme to work. I tried this:
...ANSWER
Answered 2019-Sep-27 at 13:39We are the authors of OpenMapTiles project and the repos you are linking.
If you need to use the dark-matter-gl style - the easiest is to go to https://cloud.maptiler.com/maps/darkmatter/, create a free account and copy&paste the sample viewer provided on this website.
This gives you free hosting and the style into your webpage - with a viewer of your choice, including OpenLayers.
QUESTION
Here is the layout of the simulations I am running
...ANSWER
Answered 2019-May-22 at 07:25Edit: I changed my answer after better understanding the problem.
Your problem comes from circular imports (see this tutorial for instance): your files settings_centroid.py and gizmo_read/read.py both include each other.
When you import settings_centroid.py, it imports reads.py that directly runs settings_centroid.init(), but at that point, Python didn't load all the symbols that are within settings_centroid.py, hence it doesn't find init().
Circular imports bring tricky problems to solve. My advice would be to refactor your code to avoid them, which could take a bit of time if your codebase is already big.
One option, that may not make sense with the logic of your whole code, (if it doesn't, sorry you'll have to think this through) if settings_centroid.py is something of a helper class, is to make a sub-package with it and try to limit its dependency on other modules.
If you really can't refactor, you can try to limit your imports to function scopes.
For instance, settings_centroid.py could become
QUESTION
I am trying to use the non-proprietary basemap style from openmaptiles.org (https://openmaptiles.org/docs/website/mapbox-gl-js/) with Deck.gl. In my example I am using the 'Dark matter' style.
...ANSWER
Answered 2019-Jan-16 at 00:34As you'll see when you go to that URL directly, tilehosting.com is telling you that you don't have the right API key to access that resource.
QUESTION
ANSWER
Answered 2018-May-21 at 11:15mapboxMap.setStyleJson method expects the actual JSON string, not a URL. In order to pass a URL, use mapbox map's setStyleUrl method or map view's setStyleUrl method:
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