Fasta_Tools

Author: Elise Gay (EPHE, MNHN)
Description: A collection of Python functions to parse, process, and manipulate FASTA files.

This module provides handy utilities to split, subset, deduplicate, and analyze FASTA sequences.

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Features

• Split FASTA files into chunks of n sequences
• Convert FASTA to dictionary {seq_id: sequence}
• Extract sequences by ID list
• Rename FASTA IDs using an external mapping file
• Remove duplicate sequences while keeping unique IDs
• Compute percentage of ambiguous bases (N/n) in sequences

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Installation

Clone this repository and import the module into your project:

git clone https://github.com/EliseGAY/Fasta_ToolsBox.git
cd Fasta_ToolsBox
pip install -e .

In your Python script:

import fasta_tools

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Usage

Split a FASTA file

fasta_tools.split_fasta("example.fasta", 100)

➡ Splits example.fasta into multiple smaller files with 100 sequences each.

Convert FASTA into a dictionary

d = fasta_tools.fasta_dict("example.fasta")
print(d["seq1"])

➡ Prints the sequence for ID seq1.

Extract sequences by ID

ids = ["seq1", "seq2", "seq3"]
fasta_tools.Select_Seq("example.fasta", ids, "subset.fasta")

➡ Creates subset.fasta containing only the requested sequences.

Rename FASTA IDs

fasta_tools.add_fasta_name("example.fasta", "new_ids.txt", "renamed.fasta")

➡ new_ids.txt should contain one new name per line.

Remove duplicate sequences

fasta_tools.remove_dup("example.fasta", "deduplicated.fasta")

Compute %N (ambiguous bases) per sequence

fasta_tools.get_N_percent("example.fasta")

➡ Prints sequence_ID percent_N for each sequence.

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Dependencies

• Python ≥ 3.6 (some functions also work on Python 2.7, but not recommended)
• Standard library only (sys, re)

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To Do / Known Issues

• ⚠️ split_fasta may write an extra sequence in the last file due to counter handling
• Improve memory efficiency for very large FASTA files

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