medvedevgroup / mutation-rate-intervals Goto Github PK

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I'd like to inform you that in the case of the 'BernoulliModel,' which is causing some errors (errors are listed below) while running, some correction or further development may be required. Without 'BernoulliModel,' it works fine.

Error list:
$ python3 $packg/simulate_unit_errors.py K=21 N=10000 S=4 T=2 P=0.001 B=0.6
Traceback (most recent call last):
File "/home/pijush/Desktop/mutation-rate-intervals/simulate_unit_errors.py", line 622, in
if name == "main": main()
File "/home/pijush/Desktop/mutation-rate-intervals/simulate_unit_errors.py", line 217, in main
mutationModel.set_sketch_prng(sketchSize,sketchPrngs[sketchSize])
AttributeError: 'BernoulliModel' object has no attribute 'set_sketch_prng'

$ cat FirstSeq.fasta | python3 $packg/simulate_nucleotide_errors.py K=21 S=4 T=2 P=0.001 B=0.6
the bernoulli noise model is not currently supported

$ python3 $packg/simulate_unit_errors_thm5.py K=21 L=10000 T=1 P=0.001 B=-0.6
Traceback (most recent call last):
File "/home/pijush/Desktop/mutation-rate-intervals/simulate_unit_errors_thm5.py", line 583, in
if name == "main": main()
File "/home/pijush/Desktop/mutation-rate-intervals/simulate_unit_errors_thm5.py", line 114, in main
pSubstitution = parse_probability(argVal)
File "/home/pijush/Desktop/mutation-rate-intervals/simulate_unit_errors_thm5.py", line 558, in parse_probability
raise ValueError
ValueError

$ cat $refg | python3 $packg/simulate_nucleotide_errors_thm5.py K=21 T=1 P=0.001 B=0.6 --stats='Simulated2.fasta'
the bernoulli noise model is not currently supported

Currently, to figure out what each function does, you need to consult the --h help text or in the code comments for scripts without --h. Might be helpful to have a brief description of each file. Eg. what's the difference between simulate_unit_errors_v1.py and simulate_unit_errors.py

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I found that your code generates sequences conceptually; is there any way to obtain those sequences in a *.FASTA file?