plasan 0.1

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PlasAnn

Plasmid annotation pipeline

This tool is designed for annotating plasmid sequences from FASTA or GenBank files. It utilizes various databases and tools to provide a comprehensive annotation of plasmid sequences, including the detection of coding sequences (CDS), origins of replication, transposons, and more.

Features

• When the program is run for the first time the Databases will get downloaded automatically.
• The pipeline can take single fasta file or a folder of fasta files as input.
• It can also take a genbank file or a folder of genbank files as input

Installation

Dependencies

This script requires the following Python packages:

• gdown
• argparse
• pandas
• biopython
• matplotlib
• pycirclize

Additionally, it relies on external tools such as Prodigal. Ensure these dependencies are installed:

pip install gdown pandas biopython matplotlib

Installing Prodigal

You can download and install Prodigal from its official repository: from here

Installing command line blast

Command line blast needs to be installed. Follow the installation instruction here
Remember to append the path to the new BLAST bin directory to the existing PATH setting.

Usage

To run the script, go to the script folder and then use the following command:

python annotate_plasmids.py -i <input_file_or_directory> -o <output_directory> -t <file_type>

if you are running the script from other folder be sure to specify the path to annotate_plasmid.py. For example:

python /path_to_the_main_pipeline_folder/Scripts/annotate_plasmids.py -i <input_file_or_directory> -o <output_directory> -t <file_type>

Parameters

• -i, --input: Path to the input file or directory containing FASTA or GenBank files.
• -o, --output: Path to the output directory where results will be stored.
• -t, --type: Type of the input files, either fasta or genbank.

Example Commands

For FASTA Files:

python annotate_plasmids.py -i /path/to/fasta/files -o /path/to/output/directory -t fasta

For GenBank Files:

python annotate_plasmids.py -i /path/to/genbank/files -o /path/to/output/directory -t genbank

Upon choosing GenBank as the file type, you will be prompted to select one of the following options:

1. Annotate the existing CDS in the genbank file.
2. Overwrite existing CDS in GenBank files using Prodigal.

Outputs

• CSV Tables: Contain the annotation details for each plasmid.
• GenBank Files: Annotated GenBank files with updated feature annotations.
• Plasmid Maps: PNG images representing the annotated plasmid.

This tool is for large plasmids.

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