Mini tool to calculate CG content of a FASTA sequence(s) from the command line using the URL to the .fa.gz file

This tool is designed for Unix-like systems (Linux, macOS etc.) and requires:

• bash
• Python 3.x with venv and pip
• Biopython
• wget
• gunzip (from gzip)

Make sure these are installed before running the script.

1. Clone the repository.
2. Navigate to the project directory.
3. Copy URL to .fa.gz file (for example from https://ftp.ensembl.org/pub/current_fasta/)
4. Run the script using the following command:

./fastaCG.sh <URL-to-.fa.gz-file>

For example, using the .fa.gz of a Wild Boar Y chromosome primary assembly from ensembl:

• Copy URL: https://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna.primary_assembly.Y.fa.gz
• Run the following: ./fastaCG.sh https://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna.primary_assembly.Y.fa.gz
• Select ‘y’ to overwrite existing fasta.fa file in project directory
• Outputs:

  SEQUENCE NAME: Y dna:primary_assembly primary_assembly:Sscrofa11.1:Y:1:43547828:1 REF:
  CG PERCENTAGE: 43.21%
  TOTAL FASTA LENGTH: 43547828 bases
  TIME: 0.67s

• CG percentage output at 43.21%

• When the executable ./fastaCG.sh is run with a <URL-to-.fa.gz-file> from the command line, the link is downloaded using wget, renamed to ‘fasta.fa.gz’, and then gunzipped to leave the file ‘fasta.fa’.
• This fasta.fa file is then passed on to scriptfastaCGv2.py, where the bases for the sequence(s) are counted to give a CG percentage using Biopython’s SeqIO.
• The output of scriptfastaCGv2.py gives the name of the sequence(s) from the FASTA file, followed by the CG percentage of that sequence, the total FASTA file base length, and the time taken for the .py script to run.

v1 – completed December 2024

• Manual parsing of FASTA file using string methods.
• Separately counts each base as strings ‘A’, ‘T’, ‘C’, ‘G’ in lists.
• Manually constructs sequence headers and splits on ‘>’.
• Ignored lowercase bases, occasionally leading to inaccurate percentages.

v2 – completed June 2025

• Uses Biopython’s SeqIO to parse FASTA for more biologically reliable and accurate parsing.
• Simplifies base counting logic to directly calculate CG percentage.
• Handles upper- and lower-case bases (e.g G and g) to include all bases in FASTA file.
• Includes time taken and total base count for the FASTA file.
• Slightly faster. For example on https://ftp.ensembl.org/pub/current_fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz:
  v1 – Script took 1.56s for a length of 100286799 bases (slightly overcounted)
  v2 – Script took 1.29s for a length of 100286401 bases (accurate base count)