def testSimple():
lsc.verifyPrograms(lsc.requiredPrograms, verbose = True)
def testMafJoin():
programs = ['mafJoin']
lsc.verifyPrograms(programs, verbose = True)
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
##################################################
from evolverSimControl.lib.libSimControlClasses import SimTree
import evolverSimControl.lib.libSimControl as lsc
from jobTree.scriptTree.stack import Stack
from optparse import OptionParser
import os
from sonLib.bioio import newickTreeParser
import sys
# this is the first script to run in a simulation, so it will check for the
# existance of everything the entire simulation will end up calling, not
# just the scripts or external files used by runSim.py.
lsc.verifyPrograms(lsc.requiredPrograms)
def initOptions(parser):
parser.add_option('--rootDir', dest = 'rootInputDir',
help = 'Input root directory.')
parser.add_option('--rootName', dest = 'rootName', default = 'root',
help = ('name of the root genome, to differentiate it from '
'the input Newick. default=%default'))
parser.add_option('--inputNewick', dest = 'inputNewick',
help = ('Newick tree. http://evolution.genetics.washington.edu/'
'phylip/newicktree.html'))
parser.add_option('--stepLength', dest = 'stepLength', action = "store",
type = 'float', default = 0.001,
help = 'stepLength for each cycle. default=%default')
parser.add_option('--paramsDir', dest = 'paramsDir',
help = 'Parameter directory.')
def testMafJoin():
programs = ['mafJoin']
lsc.verifyPrograms(programs, verbose=True)
def testSimple():
lsc.verifyPrograms(lsc.requiredPrograms, verbose=True)
# THE SOFTWARE.
##################################################
import evolverSimControl.lib.libSimControl as lsc
import evolverSimControl.lib.libSimControlClasses as lscc
from jobTree.scriptTree.stack import Stack
from optparse import OptionParser
import os
import re
from sonLib.bioio import newickTreeParser
from sonLib.bioio import printBinaryTree
import sys
import xml.etree.ElementTree as ET
programs = ['evolver_cvt', 'evolver_transalign', 'mafJoin']
lsc.verifyPrograms(programs)
def initOptions(parser):
parser.add_option('--simDir', dest = 'simDir',
help = 'Simulation directory.')
parser.add_option('--maxBlkWidth',dest = 'maxBlkWidth',
default = 512, type = 'int',
help = ('Maximum mafJoin maf block output size. May be reduced '
'towards 250 (or lower) for complicated phylogenies '
'with lots of dash characters in blocks or expanded out '
'for simple phylogenies. '
'default=%default'))
parser.add_option('--maxInputBlkWidth', dest = 'maxInputBlkWidth',
default = 1000, type = 'int',
help = ('Maximum mafJoin maf block input size. mafJoin will cut '
'inputs to size, may result in long runs for very simple '
# THE SOFTWARE.
##################################################
import evolverSimControl.lib.libSimControl as lsc
import evolverSimControl.lib.libSimControlClasses as lscc
from jobTree.scriptTree.stack import Stack
from optparse import OptionParser
import os
import re
from sonLib.bioio import newickTreeParser
from sonLib.bioio import printBinaryTree
import sys
import xml.etree.ElementTree as ET
programs = ['evolver_cvt', 'evolver_transalign', 'mafJoin']
lsc.verifyPrograms(programs)
def initOptions(parser):
parser.add_option('--simDir', dest='simDir', help='Simulation directory.')
parser.add_option(
'--maxBlkWidth',
dest='maxBlkWidth',
default=512,
type='int',
help=('Maximum mafJoin maf block output size. May be reduced '
'towards 250 (or lower) for complicated phylogenies '
'with lots of dash characters in blocks or expanded out '
'for simple phylogenies. '
'default=%default'))
parser.add_option(
