Repository for the laboratory of biological data mining project, Oct. 2021
Simply clone the repository
The search_significant.py script allows the user to outer merge (using pandas) the csv of the expansion lists of a gene of interest, retrieved from the gene@home portal. It merges based on the gene name to reduce complexity, so the user must take into account all isoforms listed in the final dataset when proceeding with the analysis.
Run the script with python. You must provide:
- (-i, --inputf) folder containing the csv files (not zipped)
- (-l, --list) .txt file containing the list of genes that you want to check if they appear in the merged dataframe.
Example:
python search_significant.py -i /home/elisa/LBDM-project/ACLY -l /home/elisa/LBDM-project/EMTgenes.txt
- a "significant.csv" containing the merged dataframes
- prints at command line the list of the genes from the text file provided that are present in the dataframe.