This program is a basic python conversion of Mick Watson's Ideel. It reads in one or more input FASTA files and uses prodigal for rapid annotation, then runs diamond blast on the output, then compares the query length to hit length.
It was built with the help of 'Bionitio'
This program is released as open source software under the terms of MIT License.
Clone this repository:
git clone https://github.com/alegione/pydeel
Pydeel can be installed using pip in a variety of ways:
- Inside a virtual environment:
python3 -m venv pydeel_dev
source pydeel_dev/bin/activate
pip install -U /path/to/pydeel
- Into the global package database for all users:
pip install -U /path/to/pydeel
- Into the user package database (for the current user only):
pip install -U --user /path/to/pydeel
Pydeel uses prodigal to rapidly annotate your genome and diamond to compare your annotated genome to a provided database, these are required to be installed locally for the tool to run successfully
Pydeel is a basic python conversion of Mick Watson's Ideel. It reads one or more input FASTA files and for each file it will use prodigal for rapid annotation, then run diamond blast, then compare the query length to hit length.
The outputs will be a protein annotation, a tab delimited file containing each of the best hits to the database used for Diamond (as well as the query/target ratio), and several plots. These are currently in interactive html outputs, .png can be saved after opening the files. The plots are a histogram of the query/target ratios (normal and 'zoomed in'), as well as a line plot that can reflect where in your genome the query/target ratio substantially changes.
Pydeel can display usage information on the command line via the -h or --help argument:
pydeel.py -h
usage: pydeel.py [-h] [--version] [--log LOG_FILE] -i Path/to/input.fasta
[-c 11] [-d Uniprot.dmnd] -o Path/to/output [-t TITLE]
Pydeel: a tool to investigate bacterial or viral genome assembly based on
protein lengths. Provide a fasta file and protein database as input and pydeel
will provide gene completeness ratios
arguments:
-h, --help show this help message and exit
--version show program's version number and exit
-i Path/to/input.fasta, --input Path/to/input.fasta
File (or directory) containing sequence, either in
fasta format to be annotated or pre-annotated faa
-c 11, --code 11 Translation table for input sequence (default: 11)
-d Uniprot.dmnd, --database Uniprot.dmnd
Protein database in diamond format
-o Path/to/output, --outdir Path/to/output
Name of output directory (required)
-n NAME, --name NAME Prefix/name for files (default: "yyyymmdd-hhmmss-pydeel")
-p Path/to/RefProtein.faa, --proteins Path/to/RefProtein.faa
Input protein reference to compare annotations against
-f, --force Overwrite any directories/files with the same names
present at the target
-r, --resume Continue run where last completed
pydeel will output a log file containing information about program progress to the .log file. The log file includes the command line used to execute the program, and a note indicating which files have been processes so far. Events in the log file are annotated with their date and time of occurrence.
Pydeel returns the following exit status values:
- 0: The program completed successfully.
- 1: File I/O error. This can occur if at least one of the input FASTA files cannot be opened for reading. This can occur because the file does not exist at the specified path, or pydeel does not have permission to read from the file.
- 2: A command line error occurred. This can happen if the user specifies an incorrect command line argument. In this circumstance pydeel will also print a usage message to the standard error device (stderr).
- 3: Input FASTA file is invalid. This can occur if pydeel can read an input file but the file format is invalid.
- 4: Output directory exists already and cannot be overwritten
Please submit bug reports and feature requests to the issue tracker on GitHub: