AlleleFinder
Overview
AlleleFinder is a Python-based suite of tools designed for the discovery, sequence typing, and profiling of stx alleles in Shiga toxin-producing Escherichia coli (STEC). It provides a comprehensive solution for researchers and professionals working in the field of bacterial genomics.
Features
AlleleFinder offers seven main functionalities, each represented by a separate script:
profile_reduce: Reduces full wgMLST profile from Enterobase using genes of interest.allele_translate_reduce: Translates allele files from Enterobase in nucleotide format to amino acid, performs content and length checks, and removes duplicates.allele_find: Performs BLAST analyses on a nucleotide allele database against nucleotide query sequences to discover their sequence types.allele_translate_find: Performs BLAST analyses on an amino acid database against amino acid query sequences to find matching alleles.aa_allele_find: Performs BLAST analyses on an amino acid database against amino acid query sequences to find matching alleles.allele_split: Splits a single allele database file into multiple files; one sequence per file.allele_concatenate: Concatenates alleles of the stx A and B subunits into a single sequence with a linker.stec_combined_subunits: Processes STEC alleles with both A and B subunits, performing subunit-level BLAST analyses and reporting.
Documentation
Detailed documentation for each script and general usage of AlleleFinder is available at the AlleleFinder GitHub pages site.
Quick Start
Conda is required to install AlleleFinder. See the documentation or AlleleFinder installation for instructions on getting conda installed on your system.
Create a new conda environment:
conda create -n allele_finder -c olcbioinformatics allelefinder
Additional installation instructions are available here.
Usage
Each script has specific input requirements and usage instructions. Please refer to the respective documentation for each script for detailed information:
profile_reduceallele_translate_reduceallele_findallele_translate_findaa_allele_findallele_splitallele_concatenatestec_combined_subunits
Feedback
We welcome your feedback. If you encounter any issues installing or running AlleleFinder, have feature requests, or need assistance, please open an issue on GitHub.
License
AlleleFinder is licensed under the MIT License. See the LICENSE file for more details.
1 maintainer
Release files for AlleleFinder 0.5.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| allelefinder-0.5.0.tar.gz | 119.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| allelefinder-0.5.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 297.6 kB
Release files / allelefinder-0.5.0.tar.gz
| Download URL | allelefinder-0.5.0.tar.gz |
|---|---|
| Size | 119.5 kB |
| Tags | Source |
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| Download URL | allelefinder-0.5.0-py3-none-any.whl |
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| Size | 178.1 kB |
| Tags | Python 3 |
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