This tool was designed to compare the subgenomes of the hexaploid wheat in terms of the gene structure; in other words, it performs a six-way comparison based on pairwise comparisons between the three subgenomes and reports which genes are conserved between the three.
The main Python-based parsing script (main.py) was mainly built based on Pandas and argparse. The overall pipeline (Pipeline.py) was built using SnakeMake, and utilized samtools, GMAP, Cufflinks, and Mikado.
Only Pipeline.py and main.py are necessary, tests.py was created for testing main.py.
To use the pipeline: snakemake -s Pipeline.py, given that both Pipeline.py and main.py are in the same directory.