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command-line test case:

# python3 ../../../transit.py cgi extract_counts <fastq file> <ids file> <output counts file>
    
# python3 ../../../transit.py cgi create_combined_counts <comma seperated headers> <counts file 1> <counts file 2> ... <counts file n> <combined counts file>
    
# python3 ../../../transit.py cgi extract_abund <combined counts file> <metadata file> <control condition> <sgRNA strength file> <uninduced ATC file> <drug> <days>  <fractional abundundance file>

# python3 ../../../transit.py cgi run_model <fractional abundundance file>  <CRISPRi DR results file> [-use_negatives]



> python3 ../../../transit.py cgi extract_abund RIF_D1_combined_counts.txt samples_metadata.txt DMSO sgRNA_info.txt uninduced_ATC_counts.txt RIF 1 RIF_D1.frac_abund.txt

> python3 ../../../transit.py cgi run_model RIF_D1.frac_abund.txt CDR_results.RIF_D1.txt
[cgi:run_model()] 185 Total Significant Gene Interactions 
[cgi:run_model()] 112 Significant Gene Depletions 
[cgi:run_model()] 73 Significant Gene Enrichments 

> python3 ../../../transit.py cgi run_model RIF_D1.frac_abund.txt CDR_results.RIF_D1.negsatives.txt -use_negatives
[cgi:run_model()] 2132 Total Significant Gene Interactions
[cgi:run_model()] 1042 Significant Gene Depletions
[cgi:run_model()] 1090 Significant Gene Enrichments
