Hooty: a fast DNA distance matrix tool with innovative handling of ambiguous sites

Hooty computes the minimum and maximum K2P distance between predetermined groups in an alignment and outputs results in a matrix format. It also includes an option for the interpretation of ambiguous bases.

INSTALLATION

To install Hooty, go to the GitHub repository and download the latest release.

Alternatively, you can clone the repository with the following command: git clone https://github.com/Princic-1837592/Hooty.git

EXAMPLES

Some examples can be found in the examples folder of the repository.

SYNOPSIS

python3 hooty.py <fasta_file> <partition_file> [OPTIONS] To use via graphical interface: python3 hooty_gui.py [<fasta_file>] [<partition_file>] [OPTIONS]

INPUT FILES

<fasta file> a file containing the sequences to be analyzed. Sequences must have the same length. Sequence names should refer to a name in the partition file.
>COD-001_species01                                             ├── sequence name
CACACTCTATTTAATTTTTGGTATTTGAGCCGGGCTAGTCGGAACCGGACTCRGCCTACT ──┐
AATCCGAGCAGAACTTAGTCAGCCCGGAACTTTACTAGGGGACGATCAACTATATAATGT   ├── DNA sequence
GGTTGTCACTGCTCACGCATTTATCATAATTTTCTTCTTAGTAATACCGTTAATAATTGG   │
CGGATTCGGAAATTGATTAGTCCCATTAATATTAGGTGCTCCAGATATAGCCTTTCCTCG   │
AATAAACAACATAAGATTTTGATTACTACCTCCATCACTAACACTACTATTAACCTCAGC ──┘
>COD-002_species01                                             ├── sequence name
CACACTCTATTTAATTTTTGGTATTTGAGCCGGGCTAGTCGGAACCGGACTCAGCCTACT ──┐
AATCCGAGCAGAACTTAGTCAGCCCGGAACTTTACTAGGGGACGATCAACTATATAATGT   ├── DNA sequence
GGTTGTCACTGCTCACGCATTTATCATAATTTTCTTCTTASTAATACCGTTAATAATTGG   │
CGRATTCGGAAATTGATTAGTCCCATTAATATTAGGTGCTCCAGATATAGCCTTTCCTCG   │
AATAAACAACATAAGATTTTGATTACTACCTCCATCACTAACACTACTATTAACCTCAGC ──┘
<partition file> a line separated file containing one group per line. Please pay attention to the following:
- A name can appear in only one group.
- Name matching is case-sensitive (species01 is different from Species01).
- A name should not be substring of another (having something like species1 and species11 could result in an error)
species01
species02
species03
species04

Multiple names for the same group must be on the same line, separated by commas.
species01
species02a, species02b
species03a, species03b, species03c
species04

OPTIONS

-f | --full-matrix <string> write file with pairwise distance for all sequences
-h | --help print list of commands and usage
-o | --output <string> specify name for output file. By default, the output file will be placed in the same folder as the input, with the same name but extension .csv
-p | --processes <integer> number of processes to run in parallel. Default is number of cores on the machine
-s | --separator <x> separator to use in output file. x can be tab, comma, or semicolon (default)
-t | --threshold <number> maximum percentage of ambiguous bases allowed within a group. The value must be between 0 and 1. Default is 0.0
-u | --unambiguous always treat ambiguous sites as similarities. When this is active, the threshold parameter is ignored

SYSTEM REQUIREMENTS

Hooty was developed and tested with Python version 3.10. Compatibility with previous versions has not been tested.

To use the graphical interface, the package Gooey is required. To install it, run the following command:

pip install -r requirements_gui.txt

CONTRIBUTION AND BUG REPORT

If you want to contribute to the project or report a bug, you can open a pull request or an issue on the GitHub repository

AUTHORS

Written and developed by Andrea Princic and Giacomo Chiappa, Sapienza University of Rome, Italy.