Notes.xml

Files: 
	• DREAMTEAM_WF2.py
		○ Runs through workflow on each sample
		○ Outputs list of genes that appear in samples with a frequency at or above a certain (optionally specified) threshold
	• make_samples.sh
		○ Calls gene_list_subset.py with optionally specified subset proportions 
			§ (defaults to using full gene list)
		○ Creates a specified number of sample files for each specified subset proportion
	• gene_list_subset.py
		○ Creates file with a random sampling from the input file
		○ Size is specified from the command line as a proportion of the size of the input file
	• gene_freq.py
		○ Takes as input the full output gene list CSV from DREAMTEAM_WF2.py
		○ Creates new output CSV of genes at or above a specified threshold
	• HUGOSymbol_HGNCID.txt
		○ Example gene list for sleep apnea
		○ Contains gene symbols and corresponding HGNC IDs, separated by commas 

Commands:
	• ./make_samples <input_filename> <replicates> [list_of_subset_proportions]
		○ This will automatically call gene_list_subset.py on the input file the specified number of times for each specified subset proportion (or 1.0 if no proportions specified)
		○ If you wish to run gene_list_subset.py manually, use the format:python3 gene_list_subset.py <input_filename> <proportionate_size_of_subset>
	• python3 DREAMTEAM_WF2.py [frequency_threshold]
		○ Frequency threshold will default to 0.8 if left unspecified, or if specified threshold is invalid
	• python3 gene_freq.py <full_gene_list_CSV> <number_of_samples> [frequency_threshold]
		○ Frequency threshold will default to 0.8 if left unspecified, or if specified threshold is invalid
		○ Number of samples must be the number of samples used to build the full gene list CSV
Example: 
	• Command: ./make_samples HUGOSymbol_HGNCID.txt 3 0.8 0.7 0.6
		○ Result: creation of samples directory
	• Command: python3 DREAMTEAM_WF2.py 0.6
		○ Result: creation of CSV containing IDs and appearance counts of all genes outputted by mod1a or mod1b, and another CSV with IDs and appearance counts of all genes that appeared in ≥ 60% of the 9 samples created above
	• Command: python3 gene_freq.py full_gene_counts.csv 9 0.9
		○ Result: creation of CSV containing IDs and appearance counts of all genes that appeared in ≥ 90% of the 9 samples created above