pyani | Python module for average nucleotide identity analyses

by widdowquinn Python Version: v0.2.12 License: MIT

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

kandi X-RAY | pyani Summary

pyani is a Python library. pyani has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Application and Python module for whole-genome classification of microbes using Average Nucleotide Identity.

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pyani has a low active ecosystem.

It has 155 star(s) with 55 fork(s). There are 13 watchers for this library.

It had no major release in the last 12 months.

There are 42 open issues and 194 have been closed. On average issues are closed in 208 days. There are 10 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of pyani is v0.2.12

Quality

pyani has 0 bugs and 0 code smells.

Security

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

pyani code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

pyani is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

pyani releases are available to install and integrate.

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

Installation instructions, examples and code snippets are available.

pyani saves you 1396 person hours of effort in developing the same functionality from scratch.

It has 3174 lines of code, 170 functions and 24 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

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

Report subcommands in the database
Color a string
Get matrix labels for a given run
Label the results of a single gene
Run ANIm analysis
Add genome files
Add a run to the database
Collects the expected output files in a directory
Run fastani analysis
Parse arguments
Write contigs to an Assembly
Calculate ANIm
Process a delta - filter directory
Process the input files
Run ANI
Run the dependency graph
Create ANIRESults object
Creates a heatmap from a pandas dataframe
Returns the version number of the blastall executable
Download genomes from NCBI
Index subcommand
Classify an ANI run
Build a networkx graph from the results
Download genome and hash
Write styles to a file
List installed dependencies

Get all kandi verified functions for this library.

pyani Key Features

No Key Features are available at this moment for pyani.

pyani Examples and Code Snippets

No Code Snippets are available at this moment for pyani.

Community Discussions

No Community Discussions are available at this moment for pyani.Refer to stack overflow page for discussions.

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

Vulnerabilities

No vulnerabilities reported

Install pyani

The first step is to obtain genome data for analysis. pyani expects to find each individual genome in its own FASTA file (that file can contain multiple sequences - chromosomes and plasmids; sequenced scaffolds, etc). All the FASTA files for an analysis are expected to be located in a single subdirectory (with optional labels and classes files). You can arrange your data manually, but pyani provides a subcommand that downloads all genomes in a taxon subtree from NCBI, and organises them ready for use with pyani. We'll use the pyani download subcommand to download all available genomes for Candidatus Blochmannia from NCBI. The taxon ID for this grouping is 203804. The first argument is the output directory into which the downloaded genomes will be written (-o C_blochmannia). To download anything from NCBI we must provide an email address (--email my.email@my.domain), and to specify which taxon subtree we want to download we provide the taxon ID (-t 203804). Here we also request verbose output (-v), and write a log file for reproducible research/diagnosing bugs and errors (-l C_blochmannia_dl.log).
_genomic.fna.gz: the compressed genome sequence
_genomic.fna: the uncompressed genome sequence
_genomic.fna.md5: an MD5 hash/checksum of the (uncompressed) genome sequence; this was generated during the download
_hashes.txt: a list of MD5 hashes; this is provided by NCBI and is a reference to be sure that the download did not corrupt the genome sequence

Support

If you would like to contribute code to the pyani project (e.g. a bug fix or new feature), please refer to the CONTRIBUTING.md guide for more details.

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