humann | HUMAnN 3.0 is the next generation | Genomics library

by biobakery Python Version: 3.7 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | humann Summary

humann is a Python library typically used in Artificial Intelligence, Genomics applications. humann has no bugs, it has no vulnerabilities, it has build file available and it has low support. However humann has a Non-SPDX License. You can download it from GitHub.

HUMAnN 3.0 is the next generation of HUMAnN (HMP Unified Metabolic Analysis Network). Francesco Beghini1 ,Lauren J McIver2 ,Aitor Blanco-Mìguez1 ,Leonard Dubois1 ,Francesco Asnicar1 ,Sagun Maharjan2,3 ,Ana Mailyan2,3 ,Andrew Maltez Thomas1 ,Paolo Manghi1 ,Mireia Valles-Colomer1 ,George Weingart2,3 ,Yancong Zhang2,3 ,Moreno Zolfo1 ,Curtis Huttenhower2,3 ,Eric A Franzosa2,3 ,Nicola Segata1,4. HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question "What are the microbes in my community-of-interest doing (or capable of doing)?".

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Quality

Security

License

Reuse

Support

humann has a low active ecosystem.

It has 116 star(s) with 49 fork(s). There are 14 watchers for this library.

It had no major release in the last 6 months.

There are 3 open issues and 31 have been closed. On average issues are closed in 18 days. There are 8 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of humann is 3.7

Quality

humann has no bugs reported.

Security

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

License

humann has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

humann releases are not available. You will need to build from source code and install.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed humann and discovered the below as its top functions. This is intended to give you an instant insight into humann implemented functionality, and help decide if they suit your requirements.

Check the requirements
Convert bam file to sam format
Parse the chocophlan gene index
Execute a command
Combine unaligned reads
Find the md field of the SAM data
Calculates the percent identity based on a cigar string
Update the configuration
Adds a directory to the environment
Log the settings
Build taxonomic taxonomy from features
Filter a FASTA file
R Reduce a gene table
Adds reads from a file
Parse arguments
Compute gene family
Regroup a table
Calculate coverage based on blastx
Create a custom database
Get command line arguments
Identify reactions and pathways and reactions
Merge pathways from a gene table
Join a list of gene_tables
Splits two table files
Get orthogonal orthogonal path
Read koid file

Get all kandi verified functions for this library.

humann Key Features

No Key Features are available at this moment for humann.

humann Examples and Code Snippets

No Code Snippets are available at this moment for humann.

Community Discussions

Trending Discussions on humann

Set labels of radio button group dynamically based on values selected in drop down lists

QUESTION

Set labels of radio button group dynamically based on values selected in drop down lists

Asked 2021-Nov-04 at 08:33

I have an html form with 4 form elements - 3 drop down lists and one group of radio buttons.

I want the label of the radio buttons to be set dynamically based on the values selected in the drop down lists.

Ex- The values selected in the drop down lists are q-tip, hold and h1 rspectively. So, the labels in the radio button group (Direction) should be:

First radio button - q-tip hold h1.
Second radio button - h1 hold q-tip

This is the jsfiddle link : http://jsfiddle.net/coderr/yznf1qk3/22/

...

ANSWER

Answered 2021-Nov-04 at 08:33

You need to add some HTML to make it easier to access the text

Source https://stackoverflow.com/questions/69835862

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

Vulnerabilities

No vulnerabilities reported

Install humann

You can download the latest HUMAnN 3.0 release or the development version. The source contains example files. If installing with pip, it is optional to first download the HUMAnN 3.0 source. Option 1: Latest Release (Recommended). Option 2: Development Version.
humann.tar.gz and unpack the latest release of HUMAnN 3.0
Create a clone of the repository: $ git clone https://github.com/biobakery/humann Note: Creating a clone of the repository requires Github to be installed.
Move to the HUMAnN 3.0 directory.
Install HUMAnN 3.0 $ pip install humann This command will automatically install MinPath (and a new version of glpk) along with Bowtie2 and Diamond (if they are not already installed). To bypass the install of Bowtie2 and Diamond, add the option "--install-option='--bypass-dependencies-install'" to the install command. To build Diamond from source during the install, add the option "--install-option='--build-diamond'" to the install command. To overwite existing installs of Bowtie2 and Diamond, add the option "--install-option='--replace-dependencies-install'" to the install command. If you do not have write permissions to '/usr/lib/', then add the option "--user" to the HUMAnN install command. This will install the python package into subdirectories of '~/.local' on Linux. Please note when using the "--user" install option on some platforms, you might need to add '~/.local/bin/' to your $PATH as it might not be included by default. You will know if it needs to be added if you see the following message humann: command not found when trying to run HUMAnN after installing with the "--user" option.
Move to the HUMAnN 3.0 directory $ cd $HUMAnN_PATH
Install HUMAnN 3.0 $ python setup.py install This command will automatically install MinPath (and new version of glpk) along with Bowtie2 and Diamond (if they are not already installed). To bypass the install of Bowtie2 and Diamond, add the option "--bypass-dependencies-install" to the install command. If you do not have write permissions to '/usr/lib/', then add the option --user to the install command. This will install the python package into subdirectories of '~/.local'. Please note when using the "--user" install option on some platforms, you might need to add '~/.local/bin/' to your $PATH as it might not be included by default. You will know if it needs to be added if you see the following message humann: command not found when trying to run HUMAnN after installing with the "--user" option.
Downloading the databases is a required step if your input is a filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format). If your input files will always be mapping results files (sam, bam or blastm8 format) or gene tables (tsv or biom format), you do not need to download the ChocoPhlAn and translated search databases. Download the ChocoPhlAn database providing $INSTALL_LOCATION as the location to install the database (approximate size = 16.4 GB). NOTE: The humann config file will be updated to point to this location for the default chocophlan database. If you move this database, please use the "humann_config" command to update the default location of this database. Alternatively you can always provide the location of the chocophlan database you would like to use with the "--nucleotide-database " option to humann.
Selecting a level of gene family resolution
Selecting a scope for translated search
To download the full UniRef90 database (20.7GB, recommended): $ humann_databases --download uniref uniref90_diamond $INSTALL_LOCATION
To download the EC-filtered UniRef90 database (0.9GB): $ humann_databases --download uniref uniref90_ec_filtered_diamond $INSTALL_LOCATION
To download the full UniRef50 database (6.9GB): $ humann_databases --download uniref uniref50_diamond $INSTALL_LOCATION
To download the EC-filtered UniRef50 database (0.3GB): $ humann_databases --download uniref uniref50_ec_filtered_diamond $INSTALL_LOCATION
If you have already installed HUMAnN 3.0, using the Initial Installation steps, and would like to upgrade your installed version to the latest version, please follow these steps. Since you have already downloaded the databases in the initial installation, you do not need to download the databases again unless there are new versions available. However, you will want to update your latest HUMAnN 3.0 install to point to the databases you have downloaded as by default the new install configuration will point to the demo databases. To update your HUMAnN 3.0 configuration file to include the locations of your downloaded databases, please use the following steps. Please note, after a new installation, all of the settings in the configuration file, like the database folders, will be reset to the defaults. If you have any additional settings that differ from the defaults, please update them at this time. For more information on the HUMAnN 3.0 configuration file, please see the Configuration section.
Download HUMAnN 3.0
Install HUMAnN 3.0
Update the location of the ChocoPhlAn database (replacing $DIR with the full path to the directory containing the ChocoPhlAn database) $ humann_config --update database_folders nucleotide $DIR
Update the location of the UniRef database (replacing $DIR with the full path to the directory containing the UniRef database) $ humann_config --update database_folders protein $DIR

Support

Please sign up for the HUMAnN category in bioBakery Forum if any questions or concerns. Additionally, Google user group: humann-users@googlegroups.com (Read only) is available.

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