'name': 'HapMap_pops',
'default' : HapMap3_pops,
'label' : 'Name of populations',
'description': '''Which HapMap populations to use?''',
'allowedTypes': [ListType, TupleType],
'chooseFrom': HapMap3_pops,
'validate': simuOpt.valueListOf(HapMap2_pops + HapMap3_pops),
},
{
'name': 'markerList',
'default': 'hh550v3_snptable.txt',
'label': 'Marker list file',
'description': '''A file with a list of marker names. If there are more than
one fields at a line, the rest of them are ignored.''',
'allowedTypes': [StringType],
'validate': simuOpt.valueOr(simuOpt.valueEqual(''), simuOpt.valueValidFile()),
},
{
'name': 'chroms',
'default': [2,5,10],
'label': 'Chromosomes to use',
'description': 'A list of chromosomes (1-22) to use.',
'allowedTypes': [TupleType, ListType],
'chooseFrom':range(1,23),
'validate': simuOpt.valueListOf(simuOpt.valueBetween(1, 22)),
},
{
'name': 'numMarkers',
'default': [2000,2000,2000],
'label': 'Number of markers to use',
'description': '''Number of markers to use for each chromosome. This
3. Returns the names of the files created.
"""
import simuOpt
import analysisMethods
options = [
{'name': 'formatters',
'default': [],
'chooseFrom':[x.split('.')[2] for x in analysisMethods.getAnalysisMethods()],
'label': 'Formatters',
'description': 'Names of analysis methods for which input files will be created.'
},
{'name': 'inputfile',
'default': 'rep_1.pop',
'label': 'simuPOP Population',
'allowedTypes': types.StringType,
'validate': simuOpt.valueValidFile(),
'description': 'A simupop population file to parse and format.'
}
]
short_desc = """
Main formatting function to parse simuPOP population file and output the files necessary
To run one or more analysis methods.
"""
if __name__ == "__main__":
pars = simuOpt.Params(options, short_desc)
if not pars.getParam():
sys.exit(1)
from simuPOP.utils import simulateForwardTrajectory, simulateBackwardTrajectory, migrSteppingStoneRates
import os, sys, math, types, time
options = [
{
'longarg':
'initPop=',
'default':
'init.pop',
'label':
'Initia population',
'allowedTypes':
types.StringType,
'validate':
simuOpt.valueValidFile(),
'description':
'An initial population created using script selectedMarkers.py'
},
{
'longarg':
'dumpRec=',
'default':
'',
'allowedTypes':
types.StringType,
'description':
'''This is a hidden option, if set, all recombination events will
be dumped to the specified file. Please refer to the simuPOP user's guide
for explanation of this file.'''
},
