CpG_island_identificator

CpG island identification pipeline inspired by the Gardiner-Garden and Frommer (1987) method

Executable apps

Windows and linux grafical user interface standalone programs and a linux command line program are avaliable here:

Depedences

1. python3.8 or later

2. argparse: pip3 install argparse(for the command line script)

3. pyfaidx: pip3 install pyfaidx

4. pandas: pip3 install pandas

5. Gooey: (for the gui.py script) pip install Gooey

Example code

With the following script CpG islands are identified by selecting the %GC content, Obs/Exp ratio window and step size. In this example sequence the existence of CpG islands is checked on 200 bp windows with 50 bp interval(the window moves 50bp each time):
python3 cpg_island_identificator.py -in test.fasta -out cpg_table.txt -win 200 -step 50 -gc 55.00
This script can be run also as GUI by running:
python3 cpg_island_identificator_gui.py and a window will pop up

The output file will look like: