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PRESUME_help.py
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helpdoc="""
usage: PRESUME.py [-h] [--param PARAM] [-V] [--monitor MONITOR] [-n N]
[--tree TREE] [-L L] [-f F] [--polyC] [-d D] [-s S] [-T T]
[-e E] [--gtrgamma GTRGAMMA] [-u U] [--ud UD] [--ld LD]
[-m M] [--constant CONSTANT] [--output OUTPUT] [--qsub]
[--idANC IDANC] [--tMorigin TMORIGIN] [--debug] [--bar]
[--viewANC] [--save] [--CV] [-r R] [--seed SEED]
[--inprob INPROB] [--inlength INLENGTH] [--delprob DELPROB]
[--dellength DELLENGTH] [--indels INDELS] [--dop DOP]
[--dist DIST] [--editprofile EDITPROFILE]
PRESUME.py
optional arguments:
-h, --help show this help message and exit
--param PARAM load argument file(csv file)
-V, --version
--monitor MONITOR time limit (default=None)
-n N required number of sequences: if you specified this
parameter, timelimit will be postponed until the
number of the sequence reach the specified number
(default=1)
--tree TREE file name of a guide tree in Newick format.
-L L length of sequence (default=1000)
-f F fasta file name of the common ancestor sequence.
(default: poly-C)
--polyC use polyC sequence as root
-d D doubling time of origin sequence (default=1)
-s S sigma of doubling time of origin sequence (default=0)
-T T Threashold of doubling time to be deleted (default =
1000)
-e E random deletion probability (default=0)
--gtrgamma GTRGAMMA parameters for substitution rate matrix
GTR{A-C/A-G/A-T/C-G/C-T/G-T} +FU{piA/piC/piG/piT}
+G4{shape of gamma distribution} Or, you can use
default parameters by "--gtrgamma default" default:
GTR{0.3333/0.3333/0.3333/0.3333/0.3333/0.3333}
+FU{0.25/0.25/0.25/0.25} +G4{10000}
-u U upper limit of number of sequences (default=2^20)
--ud UD upper limit of doubling time (default=10^10)
--ld LD lower limit of doubling time (default=10^(-5))
-m M mean of relative subtitution rate according to gamma
distribution (default=1)
--constant CONSTANT fixed mutation rate of each site (default=None)
--output OUTPUT output folder (default:current directory)
--qsub activate preparation for distributed processes
(defalt=inactivated)
--idANC IDANC corresponging ancestral sequence (in upstream tree),
in case of distributed computing (default=None)
--tMorigin TMORIGIN birth time of origin sequence
--debug inactivate deletion of intermediate files
--bar deactivate unstable functions
--viewANC generate fasta of ancestoral sequences
--save generate args.csv
--CV sigma use as CV(Coefficient Variance) of Normal
Distribution
-r R limit of retrying simulation (default=100000)
--seed SEED random seed used to initialize the pseudo-random
number generator
--inprob INPROB file name of insertion probability for each position
--inlength INLENGTH file name of insertion length distribution
--delprob DELPROB file name of deletion probability for each position
--dellength DELLENGTH
file name of insertion length distribution
--indels INDELS file name of indels accumulated before simualtion (for
distributed computing mode)
--dop DOP Option of qsub for downstream simulation (for
distributed computing mode)
--dist DIST Distribution of d or 1/d (permissive values: 'norm',
'lognorm', 'gamma', 'gamma2') (default: 'gamma2)
--editprofile EDITPROFILE
file name of a base editing profile.
"""
def help_description():
return helpdoc
if __name__=="__main__":
pass