working with mgMap

Move file to the mgmap folder and run the following command for input file contains genomics coordinates of mutations

• python3 mgmap.py -nc inputfile

For input file, with protein level residue alterations, run the following command:

• python3 mgmap.py -g inputfile

Expected output should contain the following files:

1. file with (i) proteins or gene names (depending on the input file) with (ii) mutations of interest, (iii) functional or regulatory regions where these mutations can be mapped, (iv) conservation of each mutated residue position see here.
2. graph showing the number of mutations per gene/protein and conservation of each mutated positions
3. files containing the output for the following analyses:
   bq. GO term enrichment test
   bq. biological pathways enrichment text
   bq. biological processes enrichment text
   bq. significantly mutated protein functional or genome regulatory regions .

1. All the files (text and png) are saved in the output folder with the same name as input file.
2. For the better view, we also generate an elegant html page contains all the visualizations, to observe the all the analyses and develop hypothesis in a seamless way.