# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'jmdelarosa@cnb.csic.es'
# *
# **************************************************************************
from pyworkflow.protocol.params import (PointerParam, MultiPointerParam,
IntParam, EnumParam)
from .protocol_pkpd import ProtPKPD
from pkpd.objects import PKPDExperiment
[docs]class ProtPKPDSplitGather(ProtPKPD):
""" Split an experiment into small pieces, or gather these small pieces into an experiment.\n
Protocol created by http://www.kinestatpharma.com
"""
_label = 'split/gather experiment'
def _defineParams(self, form):
form.addSection('Input')
form.addParam('splitOrGather', EnumParam, label="Operation", choices=['Split','Gather'], default=0)
form.addParam('inputExperiment', PointerParam, label="Experiment to split", pointerClass='PKPDExperiment',
allowsNull=True, condition='splitOrGather==0')
form.addParam('groupSize', IntParam, label="Group size", default=5, condition='splitOrGather==0')
form.addParam('inputExperiments', MultiPointerParam, label="Experiments to gather", pointerClass='PKPDExperiment',
allowsNull=True, condition='splitOrGather==1')
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions --------------------------------------------
[docs] def createSubGroup(self, g, experiment, listOfSamples):
newExperiment = experiment.subset(listOfSamples)
self.writeExperiment(newExperiment, self._getPath("experiment%05d.pkpd"%g))
self._defineOutputs(**{"outputExperiment%d"%g: newExperiment})
self._defineSourceRelation(self.inputExperiment, newExperiment)
[docs] def createOutputStep(self):
if self.splitOrGather.get()==0:
experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
listOfSamples=[]
g=1
for sampleName in experiment.samples:
listOfSamples.append(sampleName)
if len(listOfSamples)==self.groupSize.get():
self.createSubGroup(g, experiment, listOfSamples)
listOfSamples=[]
g+=1
if len(listOfSamples)!=0:
self.createSubGroup(g, experiment, listOfSamples)
else:
newExperiment = PKPDExperiment()
for ptrExperiment in self.inputExperiments:
newExperiment.gather(self.readExperiment(ptrExperiment.get().fnPKPD))
self.writeExperiment(newExperiment, self._getPath("experiment.pkpd"))
self._defineOutputs(outputExperiment=newExperiment)
for ptrExperiment in self.inputExperiments:
self._defineSourceRelation(ptrExperiment, newExperiment)