forked from yachielab/PRESUME
-
Notifications
You must be signed in to change notification settings - Fork 0
/
PRESUME_help.py
68 lines (65 loc) · 2.87 KB
/
PRESUME_help.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
helpdoc="""
Usage:
PRESUME.py
[-v] [--version] [-h] [--help] [-n sequence_number] [-L sequence_length] [-s standard_deviation]
[-e extinction_probability] [--gtrgamma model_parameters] [-m mean_substitution_rate]
[--timeind substitution_probability] [--qsub] [--output directory_path] [-f input_file]
[--load file_name] [-u sequences_number] [--debug] [--bar] [--save]
[-r max_retrial_number] [--seed random_seed] [--limit time_limit]
Options:
-v --version
Print PRESUME version; ignore all the other parameters
-h --help
Print the usage of PRESUME; ignore all the other parameters
-n <Integer>
Number of sequences to be generated. Default: 100
-L <Integer>
Length of sequences to be generated. Default: 1000
-s <Float>
Standard deviation of propagation speed. Default: 0
-e <Float>
Probability of extinction. Default: 0
--gtrgamma <String>
Execute GTR-Gamma model to simulate sequence diversification with its parameters
Parameter format: --gtrgamma GTR{A-C/A-G/A-T/C-G/C-T/G-T}+FU{piA/piC/piG/piT}+G{alpha}
For more details, see https://github.com/yachielab/PRESUME/blob/master/SubstitutionModelDetails.PRESUME.pdf
or you can use the default parameter set by
--gtrgamma default
which is equivalent to
--gtrgamma GTR{0.03333/0.03333/0.03333/0.03333/0.03333/0.03333}+FU{0.25/0.25/0.25/0.25}+G4{10000}
-m <Float>
Mean of gamma distribution for relative substitution rates of different sequence
Positions. Default: 1
--constant <Float>
Execute time-independent model to simulate sequence diversification with a parameter of
constant substitution probability per generation of every sequence position
--qsub
Execute the distributed computing mode
--output <String>
Output directory path. PRESUME creates a directory unless exists. Default: current
directory
-f <String>
Input FASTA file name for the root sequence. Random sequence will be generated
unless specified
--param <String>
Basic parameter values of PRESUME can be input as a csv file (the format of the file is same
for which is output by PRESUME when -–save is specified)
-u <Integer>
Maximum number of sequences to be generated. Default: 1000000000
--debug
Output intermediate files
--bar
Activate the monitoring of simulation progress with Python tqdm module
--save
Output basic parameter values used
-r <Integer>
Maximum number of retrials of simulation when all sequences are extinct
--seed <Integer>
Seed number for generation of random values. Default: 0
--monitor <float>
Monitoring paramater. Default: 1
"""
def help_description():
return helpdoc
if __name__=="__main__":
pass