diff --git a/README.md b/README.md index 5d96d8cca785a0e575e0697d20158207f6149304..86635e960a35ee675dce30702876c64c1275af1d 100644 --- a/README.md +++ b/README.md @@ -387,6 +387,10 @@ window\_size\_subgenome3 -wup window\_up -wdwn window\_down Note: Before running main\_script.py, you need to run the SyntenyLink\_bf.pl and SyntenyLink\_st.pl scripts +To run SyntenyLink\_sb.py you can simply use: + + $ python3 main_script.py -i abc_synteny.success.colinear -g -m -n -gt abc_groundtruth.xlsx -c abc_synteny.all.chains -bl abc_blastn.blast -a1 -a1 -a1 -a2 -a2 -a2 -ws1 -ws2 -ws3 -wup -wdwn + \- Output The execution of main\_script outputs all the output files of the above scripts in the same directory as the input file. @@ -398,6 +402,10 @@ placement of genes in subgenomes when there is a ground truth file. \- Usage One read in file: abc\_groundtruth.xlsx +To run SyntenyLink\_sb.py you can simply use: + + $ python3 SyntenyLink_acc.py abc_groundtruth.xlsx + \- Output The execution of SyntenyLink\_sb prints the subgenome placemnet accuracy of each subgenome @@ -408,5 +416,5 @@ placemnet accuracy of each subgenome > subgenome3: 65.30% Exact match number for subgenome3: 5635 Missing > genes for subgenome3: 2995 -:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: - Example +=======