atlas | ATLAS - Three commands to start analyzing your metagenome data | Genomics library

 by   metagenome-atlas Python Version: v2.16.2 License: BSD-3-Clause

kandi X-RAY | atlas Summary

kandi X-RAY | atlas Summary

atlas is a Python library typically used in Artificial Intelligence, Genomics, Docker applications. atlas has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can install using 'pip install atlas' or download it from GitHub, PyPI.

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              atlas has a highly active ecosystem.
              It has 313 star(s) with 88 fork(s). There are 18 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 9 open issues and 380 have been closed. On average issues are closed in 481 days. There are 5 open pull requests and 0 closed requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of atlas is v2.16.2

            kandi-Quality Quality

              atlas has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              atlas is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              atlas releases are available to install and integrate.
              Deployable package is available in PyPI.
              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 atlas and discovered the below as its top functions. This is intended to give you an instant insight into atlas implemented functionality, and help decide if they suit your requirements.
            • Return a setuptools command class
            • Get the project root directory
            • Split a fasta file into subsets
            • Extract the version information
            • Create a configuration object from a root
            • Create plots for the quality plot
            • Draws the average quality score plot
            • Convert a pandas DataFrame to a table
            • Generate a plot for read quality reads
            • Create a FASTA file for each bin
            • Convert a Pandas DataFrame into a table
            • Run predict_genes
            • Reads a bbplit coverage file
            • Get sruntable from given identifiers
            • Run download
            • Get SRA URL from a run accession
            • Parse comments from a file
            • Combine coverage files into a single dataframe
            • Scan the contents of setup py py py
            • Splits a FASTA file into subsets
            • Create the versioneer config file
            • Extract version information from VCS
            • Run a snakemake workflow
            • Return a dictionary of sample files
            • Prepare the sample table for writing
            • Validate the merged runinfo table
            • Parse arguments from terminal
            Get all kandi verified functions for this library.

            atlas Key Features

            No Key Features are available at this moment for atlas.

            atlas Examples and Code Snippets

            No Code Snippets are available at this moment for atlas.

            Community Discussions

            QUESTION

            How to properly connect to MongoDB using Cloud functions?
            Asked 2022-Mar-25 at 16:08

            I would like to connect to my Atlas cluster only once per instance running Cloud Functions.

            Here is my code for an instance :

            ...

            ANSWER

            Answered 2022-Mar-25 at 16:08

            You can store your database client as a global variable. From the documentation,

            Cloud Functions often recycles the execution environment of a previous invocation. If you declare a variable in global scope, its value can be reused in subsequent invocations without having to be recomputed.

            Try refactoring the code as shown below:

            Source https://stackoverflow.com/questions/71353766

            QUESTION

            Phaser 3: Spritesheet doesn't load correctly
            Asked 2022-Feb-23 at 05:57

            I tried to add a spritesheet to my Phaser game the same way I've done it a few times before, however this time it seems to not load the images correctly, causing it to display a black & green square instead and causing it to throw an error when trying to play an animation.

            Can anyone tell what is causing this issue?

            (Warning: Playing the Code here seems to freeze up your browser for a few seconds, alternatively view on JSFiddle: https://jsfiddle.net/cak3goru/4/ )

            ...

            ANSWER

            Answered 2022-Feb-23 at 05:57

            The problem is, that you are using the wrong function, you should use this.anims.generateFrameNames, and not this.anims.generateFrameNumbers.

            And set the correct key clean for the sprite.
            the line should be:

            Source https://stackoverflow.com/questions/71225698

            QUESTION

            curl to fetch with digest flag
            Asked 2022-Feb-19 at 15:18

            There has been other questions on the subject, but nothing seems working for me.
            I have a functional CURL, but I want to translate to JS (with Node).

            CURL ...

            ANSWER

            Answered 2022-Feb-19 at 13:04
            PHP

            You need to specify that it's a digest:

            Source https://stackoverflow.com/questions/71148572

            QUESTION

            Connect mongodb compass with node.js
            Asked 2022-Feb-19 at 08:53

            I'm trying to connect a nodejs with mongodb using mongo db compass and im getting the following error:

            ...

            ANSWER

            Answered 2021-Nov-21 at 14:18

            For first, you have double quotes in the connection variable. Secondly: it seems to me that mongoUri should include the username and password in the query string, right?

            Source https://stackoverflow.com/questions/70055282

            QUESTION

            pymongo [SSL: CERTIFICATE_VERIFY_FAILED]: certificate has expired on Mongo Atlas
            Asked 2022-Jan-29 at 22:03

            I am using MongoDB(Mongo Atlas) in my Django app. All was working fine till yesterday. But today, when I ran the server, it is showing me the following error on console

            ...

            ANSWER

            Answered 2021-Oct-03 at 05:57

            This is because of a root CA Let’s Encrypt uses (and Mongo Atals uses Let's Encrypt) has expired on 2020-09-30 - namely the "IdentTrust DST Root CA X3" one.

            The fix is to manually install in the Windows certificate store the "ISRG Root X1" and "ISRG Root X2" root certificates, and the "Let’s Encrypt R3" intermediate one - link to their official site - https://letsencrypt.org/certificates/

            Copy from the comments: download the .der field from the 1st category, download, double click and follow the wizard to install it.

            Source https://stackoverflow.com/questions/69397039

            QUESTION

            MongoDB - How to use substitute value when there is missing field-and-value pair
            Asked 2022-Jan-23 at 13:14

            I have a documents in MongoDB Atlas with this structure:

            ...

            ANSWER

            Answered 2022-Jan-21 at 20:00

            QUESTION

            Unable to copy a database from one mongodb account to another
            Asked 2022-Jan-22 at 21:25

            I usually create a copy of a database in the same cluster in the same account like this:

            1. DUMP THE ORIGINAL DATABASE

            mongodump --uri 'mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --forceTableScan

            1. RESTORE THE DATABASE FROM THE DUMP FILE

            mongorestore --uri 'mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --nsFrom='ORIGINAL_DATABASE_NAME.' --nsTo='NEW_DATABASE_NAME.'

            And that works perfectly.

            Now, I created a new MongoDB atlas account, and I am trying to copy the original database into the new account.

            So the first step is similar:

            1. DUMP THE ORIGINAL DATABASE

            mongodump --uri 'mongodb+srv://ORIGINAL_ACC_USER_NAME:ORIGINAL_ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --forceTableScan

            1. RESTORE THE DATABASE FROM THE DUMP FILE

            Here I could not find which params to use.
            In the first example, in the second step, the URI is like this:

            mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME

            So I obviously should replace

            ACC_USER_NAME:ACC_USER_PASSWORD

            with

            NEW_ACC_USER_NAME:NEW_ACC_USER_PASSWORD

            But, what about the ORIGINAL_DATABASE_NAME, I could not find an equivalent to put there. The rest of the params:

            --archive="DUMP_FILE_NAME" --nsFrom='ORIGINAL_DATABASE_NAME.' --nsTo='NEW_DATABASE_NAME.'

            should remain the same.

            ...

            ANSWER

            Answered 2022-Jan-22 at 21:25
            Step 1

            First, you should do mongodump. You already did that correctly.

            Source https://stackoverflow.com/questions/70785706

            QUESTION

            Azure Static Web App: transform Blazor webassembly appsettings.json in Azure DevOps
            Asked 2022-Jan-06 at 09:09

            I have a static blazor web app that has the following structure:

            and the following setting in appsettings.json:

            ...

            ANSWER

            Answered 2021-Dec-01 at 07:57

            I don't think it's possible to manipulate the configuration file during the build/deployment that happens within the Oryx-container. What you could do is to manipulate the file during the pipeline run by, for example, tokenizing the environment-specific configuration values and replacing the tokens during the pipeline run. To achieve this with single json-file (ie. having just a file with the localhost-value stored in version control) you could use tokenizer- and replace tokens -task from Colin's ALM Corner extension collection (https://marketplace.visualstudio.com/items?itemName=colinsalmcorner.colinsalmcorner-buildtasks). Another option would be to have multiple environment-specific configuration files in version control and just copying a specific one over the appsettings.json during the pipeline run.

            Not sure if Static Web App environment variables could be utilized here, but adding it here if someone using GitHub Actions is looking for this - they are not yet supported by Azure Pipelines.

            https://docs.microsoft.com/en-us/azure/static-web-apps/build-configuration?tabs=github-actions#environment-variables

            Source https://stackoverflow.com/questions/70162453

            QUESTION

            Clamp geodesic to min/max latitude with d3
            Asked 2021-Dec-04 at 08:19

            I am using d3 to plot a route on a map:

            ...

            ANSWER

            Answered 2021-Dec-04 at 07:31

            A clipping function won't achieve the correct effect as it will cut your features not coerce them to follow that line.

            Instead, we can combine your projection with a geotransform to force the line to adhere to rules within the projected space:

            Source https://stackoverflow.com/questions/70220638

            QUESTION

            Can't install Matplotlib on Python 3.10 after its release (2021-10-05)
            Asked 2021-Nov-06 at 23:20

            After the release of Python 3.10, I reinstalled my modules for the newest version and I'm getting some trouble. First of all I tried to pip Numpy as it's the required one for matplotlib. But I got this problem:

            ...

            ANSWER

            Answered 2021-Nov-06 at 23:20

            As others have stated, Python 3.10 is not currently compatible with Matplotlib. You need to install and use Python 3.9 until it is supported. Until then you have a few options:

            Windows

            You can use the Python Launcher for Windows (py.exe) script to choose which Python version to run like so:

            py.exe script help: py -h

            List all installed versions py -0

            Use a specified version py -3.9

            e.g. 1 Create a virtual environment using python 3.9 py -3.9 venv .venv

            e.g. 2 install matplotlib with pip using python 3.9 py -3.9 -m pip install matplotlib

            Linux

            On Linux you can run whatever Python version you like like so:

            python3.9

            You can set up a local (your working directory and all sub-directories) virtual environment that will use your specified version like so:

            python3.9 -m venv .venv

            Which will set the version of python used to 3.9 while in the local directory, and allow you to type python instead of python3.9 each time you need it.

            Another relevant and helpful post by Rotareti here.

            Please note that I have not described how to activate and use Python Virtual Environments here in detail, for more information on using them read the python docs.

            Reference this answer if you're interested in installing a matplotlib release candidate.

            Source https://stackoverflow.com/questions/69466552

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

            Vulnerabilities

            No vulnerabilities reported

            Install atlas

            You can install using 'pip install atlas' or download it from GitHub, PyPI.
            You can use atlas 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 .
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            CLONE
          • HTTPS

            https://github.com/metagenome-atlas/atlas.git

          • CLI

            gh repo clone metagenome-atlas/atlas

          • sshUrl

            git@github.com:metagenome-atlas/atlas.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link

            Consider Popular Genomics Libraries

            Try Top Libraries by metagenome-atlas

            genome-annotator

            by metagenome-atlasPython

            Atlas2Anvio

            by metagenome-atlasPython

            virome_atlas

            by metagenome-atlasPython

            genecatalog_atlas

            by metagenome-atlasPython

            genome_atlas

            by metagenome-atlasPython