Manage your fasta files
Project description
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 (if computed) will be saved in the stats
directory. Plots (if generated) 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
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