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Step3_generate_csv.groovy
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/*******************************************************************************
* Copyright (C) 2020, Duderstadt Lab
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
******************************************************************************/
#@ MoleculeArchive archive
#@OUTPUT MarsTable table
#@ ImageJ ij
import de.mpg.biochem.mars.molecule.*;
import de.mpg.biochem.mars.table.*;
import de.mpg.biochem.mars.molecule.commands.*
import de.mpg.biochem.mars.util.*
import org.scijava.table.*
import java.util.concurrent.ConcurrentHashMap
import java.util.concurrent.ConcurrentMap
import java.io.File
// Defining columns
class RatesObs {
double posburstRate
double posburstPosition
double negburstRate
double negburstPosition
double Force
String UIDCol
String tag
}
Gyrase_Reaction = archive.getMetadata(0).getRegion("Gyrase Reaction")
//PosCycles calculation
def observations = new ConcurrentHashMap<String, RatesObs>()
archive.getMoleculeUIDs().parallelStream()\
.filter{ UID -> archive.moleculeHasTag(UID, "singleTether")}\
.filter{ UID -> archive.moleculeHasTag(UID, "coilable2p5")}\
//.filter{ UID -> !archive.moleculeHasTag(UID, "stuckForce")}\
.forEach{ UID ->
Molecule molecule = archive.get(UID)
MarsTable table = molecule.getTable()
if (table == null)
return
// if (molecule.getParameter("activity_score") < 12)
// return
RatesObs obs = new RatesObs()
obs.UIDCol = UID
if (molecule.hasTag("script_bead_loss_gyrase") &&\
molecule.hasTag("bead_loss_manual"))
obs.tag = "reactionBreak"
//else if (molecule.hasTag("manual_torque"))
//obs.tag = "torqueBreak"
else
obs.tag = "noBreak"
obs.Force = molecule.getParameter("Force_PL35")
//set defaults
obs.posburstRate = Double.NaN
obs.posburstPosition = Double.NaN
obs.negburstRate = Double.NaN
obs.negburstPosition = Double.NaN
//positive coil slope burst
if (!Double.isNaN(molecule.getParameter("pos_coil_slope"))) {
double timeWindowSize = 12.5
double startTime = archive.getMetadata(0).getPlane(0, 0, 0, (int) Gyrase_Reaction.getStart()).getDeltaTinSeconds()
double endTime = archive.getMetadata(0).getPlane(0, 0, 0, (int) Gyrase_Reaction.getEnd()).getDeltaTinSeconds()
if (table.getValue("Time_(s)", table.getRowCount()-1) < endTime) {
endTime = table.getValue("Time_(s)", table.getRowCount()-1) - 4
}
//First find max value position and set as new end point
double newEndPoint = endTime
double gMax = 0
for (int row=0; row<table.getRowCount();row++) {
double start = table.getValue("Time_(s)", row)
double end = table.getValue("Time_(s)", row) + timeWindowSize
if (start >= startTime && end <= endTime) {
double cMax = table.getValue("poscyclesG", row)
if (gMax < cMax) {
gMax = cMax
newEndPoint = table.getValue("Time_(s)", row)
}
}
}
endTime = newEndPoint
double maxRate = 0
double maxPos = 0
double[] linearFit = new double[4]
for (int row=0; row<table.getRowCount();row++) {
double start = table.getValue("Time_(s)", row)
double end = table.getValue("Time_(s)", row) + timeWindowSize
if (start >= startTime && end <= endTime) {
linearFit = table.linearRegression("Time_(s)", "poscyclesG", start, end)
if (maxRate < linearFit[2]) {
maxRate = linearFit[2]
maxPos = table.getValue("Time_(s)", row) + timeWindowSize/2
}
}
}
obs.posburstRate = maxRate
obs.posburstPosition = maxPos
}
//negative coil slope burst
if (!molecule.hasTag("chi") && !Double.isNaN(molecule.getParameter("neg_coil_slope"))) {
double timeWindowSize = 25
double startTime = archive.getMetadata(0).getPlane(0, 0, 0, (int) Gyrase_Reaction.getStart()).getDeltaTinSeconds()
double endTime = archive.getMetadata(0).getPlane(0, 0, 0, (int) Gyrase_Reaction.getEnd()).getDeltaTinSeconds()
if (table.getValue("Time_(s)", table.getRowCount()-1) < endTime) {
endTime = table.getValue("Time_(s)", table.getRowCount()-1) - 4
}
//First find min value position and set as new start point
double newStartPoint = startTime
double gMin = 100000
for (int row=0; row<table.getRowCount();row++) {
double start = table.getValue("Time_(s)", row)
double end = table.getValue("Time_(s)", row) + timeWindowSize
if (start >= startTime && end <= endTime) {
double cMin = table.getValue("negcyclesG", row)
if (gMin > cMin) {
gMin = cMin
newStartPoint = table.getValue("Time_(s)", row)
}
}
}
startTime = newStartPoint
double maxRate = 0
double maxPos = 0
double[] linearFit = new double[4]
for (int row=0; row<table.getRowCount();row++) {
double start = table.getValue("Time_(s)", row)
double end = table.getValue("Time_(s)", row) + timeWindowSize
if (start >= startTime && end <= endTime) {
linearFit = table.linearRegression("Time_(s)", "negcyclesG", start, end)
if (maxRate < linearFit[2]) {
maxRate = linearFit[2]
maxPos = table.getValue("Time_(s)", row) + timeWindowSize/2
}
}
}
obs.negburstRate = maxRate*(-1)
obs.negburstPosition = maxPos
}
observations.put(UID, obs)
}
ratesTable = new MarsTable()
ratesTable.add(new DoubleColumn("PosBurstRate"))
ratesTable.add(new DoubleColumn("PosBurstPosition"))
ratesTable.add(new DoubleColumn("NegBurstRate"))
ratesTable.add(new DoubleColumn("NegBurstPosition"))
ratesTable.add(new DoubleColumn("Force"))
ratesTable.add(new GenericColumn("UID"))
ratesTable.add(new GenericColumn("Tag"))
int row = 0
for (RatesObs obs : observations.values()) {
ratesTable.appendRow()
ratesTable.setValue("PosBurstRate", row, obs.posburstRate)
ratesTable.setValue("PosBurstPosition", row, obs.posburstPosition)
ratesTable.setValue("NegBurstRate", row, obs.negburstRate)
ratesTable.setValue("NegBurstPosition", row, obs.negburstPosition)
ratesTable.setValue("Force", row, obs.Force)
ratesTable.setValue("UID", row, obs.UIDCol)
ratesTable.setValue("Tag", row, obs.tag)
row++
}
ratesTable.saveAsCSV(archive.getFile().getParent() + "/Gyrase_Scatter.csv")
println("Generated rates table for " + archive.getFile().getName())
println("Done!!!")