Fasta_summary

A small, dependency-free Python command-line tool that summarizes a FASTA file: it counts the number of sequences and prints their mean length.

Installation

From PyPI (once published):

pip install fasta-summary-songwei

From source:

git clone https://github.com/songwei/fasta-summary.git
cd fasta-summary
python -m pip install -e .

Requires Python 3.9 or newer.

Usage

Run the command against a FASTA file:

fasta-summary example.fasta

Typical output (TSV, two lines):

sequences	3
mean_length	8.33

You can also invoke it as a module:

python -m fasta_summary example.fasta

Help:

fasta-summary --help

usage: fasta-summary [-h] input

Summarize a FASTA file: count sequences and compute mean length.

positional arguments:
  input       Path to the input FASTA file

options:
  -h, --help  show this help message and exit

Input / Output

• Input: a FASTA file. Headers start with >. Sequences may span multiple lines. Blank lines are ignored.
• Output: two TSV lines written to stdout:
  • sequences<TAB><count>
  • mean_length<TAB><mean> (mean is formatted with 2 decimal places)

Special cases

• Empty file (or file containing only blank lines): prints sequences\t0 and mean_length\t0.00 and exits with code 0.
• Missing file: prints a friendly error to stderr and exits with code 1.
• Sequence data before any header: prints a clear error to stderr and exits with code 2.

Known Limitations

• Reads the whole file into memory; not optimized for very large FASTA files.
• Length is counted in raw characters; letters are not validated against any biological alphabet (IUPAC, etc.).
• Header metadata (anything after the first whitespace) is ignored.
• Only standard >-prefixed FASTA headers are recognized; alternate formats such as FASTQ or multi-record line-wrapping conventions are not supported.
• Input is read as UTF-8 text; binary FASTA files are not supported.