The script run_single_shoebox.py generates numerous output files, all stored in the folder declared by the "-o" argument. The generated files include the following:
active_duration.txt --> Active durations for each run. Each line has three entries of the form run_number,active_duration,total_length. The units of active_duration and total_length are Python timesteps. For Control, total_length is 1850 and not 2000 because gene induction and activation start at t_induction_on = t_activation_on = 150
ddist_active.txt
ddist_approaching.txt
ddist_induced.txt
ddist_receding.txt
dist_active.txt
dist_approaching.txt
dist_induced.txt
dist_receding.txt
gene_stats.txt --> columns: is gene in contact with cluster (0 or 1),"+str(d*sig_chromatin)+", Ser5P around gene, Ser2P around gene
The description of the content of those files is needed. So far, I managed to figure out only the content of the "active_duration.txt" file, and also partially the "gene_stats.txt".
For "gene_stats.txt", however, two things are still unclear:
what is the meaning of "+str(d*sig_chromatin)+"
last column should be Ser5P/Ser2P around GENE, or around PROMOTER?
The script run_single_shoebox.py generates numerous output files, all stored in the folder declared by the "-o" argument. The generated files include the following:
run_number,active_duration,total_length. The units ofactive_durationandtotal_lengthare Python timesteps. For Control,total_lengthis 1850 and not 2000 because gene induction and activation start att_induction_on = t_activation_on = 150The description of the content of those files is needed. So far, I managed to figure out only the content of the "active_duration.txt" file, and also partially the "gene_stats.txt". For "gene_stats.txt", however, two things are still unclear: