Script used to overlap palindrome analyses with given feature files.

This module uses python3 with help of these following libraries:

• numpy
• pandas
• xlsxwriter = openpyxl

All dependant libs are listed in the requirements.txt file. To install them, use the following command:

python3 -m pip install -r requirements.txt

The script merges palindrome analysis files in the palindromes folder with annotations from NCBI in the features folder.

The result is stored in comparison folder as detailed format in {ncbi_id}.txt file or in excel file {ncbi_id}.xlsx. The excel file has 2 worksheets, one detailed for every feature and the second in a form of merged results. Finally there is a overall.xlsx file which cointains merged data from every feature alltogether.

The graphic output for comparison is only available when comparing two analysis together. The graphical overlap will be made between the analysis and with a feature table aswell.

Because of optimalisation, {ncbi_id}.xlsx files already present in comparison directory will not be analysed and processed again. This enables users to stop the analysis and continue where they stopped whenever they need to.

You can run the script as follows:

• python3 main.py -c rloop, which overlaps all available analysis files in features directory with those in rloops directory, or
• python3 main.py -i <ncbi-id> -c g4 rloop, which runs the analysis only for the selected ncbi and overlaps g-quadruplexes with r-loops.

Single analysis name for the --cmp argument always overlaps with features.

If any problem occurs, try deleting everything in the results folder and then run the command again.