FASTA manager

The FASTA Manager is a versatile command-line tool designed to assist in the management and analysis of DNA or protein sequences stored in FASTA format. This tool provides functionalities for formatting, transforming, and generating statistics or plots from sequence data.

Installation

You can install this program using pip with:

pip install fasta-manager

Command Line Arguments

--dremove: Remove duplicate sequences.

--drename: Rename duplicate sequences.

--reverse: Reverse sequences.

--complement: Complement sequences.

--rc: Reverse complement sequences.

--stats: Compute statistics.

--casefile: Case transformation (original, upper, lower).

--plots: Generate plots.

Examples

Example 1: Remove duplicates and generate statistics

fasta --dremove --stats

Example 2: Reverse complement sequences and generate plots

fasta --rc --plots

Example 3: Perform case transformation

fasta --casefile upper

You can also combine parameters where order doesn't matter.

fasta --stats --plots --casefile lower --drename

Results

The processed sequences will be stored in the results directory, and statistics will be saved in the stats directory. Plots will be saved in the plots directory

Input File Format

The input files are expected to follow the format:

>ID
Sequence

Example

test_1.fasta

>S1
actgACTG
>S2
ctgaCTGA
>S3
gggaGGGA