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‎util/chromflock_gen‎

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#!/bin/bash
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set -e
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# This is the complete workflow for chromflock
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#
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# Along the run, the overall progress can be read from status.txt
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# The progress from gnu parallel can be found in parallel.log
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#
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# Tips:
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# If this script does not finish, see how far it went by starting it with
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# $ bash -x chromflock_gen
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### SETTINGS
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## Input Files
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# The file with input probabilities, given as 64 bit doubles
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aFile="./A.double"
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# File specifying chromosome Labels use 1 for chr1, ...
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lFile="./L.uint8"
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# The file with radial values, given as 64 bit doubles. Use `nan` or `inf` for missing values.
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# NOTE: not used unless kRad is set in the lua script.
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# rFile="G.double"
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rFile=""
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# OPTIONAL: specify the proportion of structures that should be assigned each radial constraint
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# i.e., the probability in the same sense as the A matrix. If this is set each structure will
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# have an own R-file -- generated and updated by aflock in the same way as the W matrices.
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# prFile="../prFile.double"
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# NOT supported for diploid experiments!
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prFile=""
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## Input Parameters
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# Number of parallel jobs
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nCores=4
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# Number of structures to generate
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nStruct=128
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## GEOMETRY
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# Volume quotient, i.e. volume of all beads/volume of nuclei
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# Note that the bead radius can be set with -R
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# Alber uses vq=0.2
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vq=0.2
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# For ellipsoid, set the axes lengths below, if not set a spherical
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# geometry is used with ea=eb=ec=1
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# Note that 1=ea>=eb>=ec>0
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ea=
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eb=
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ec=
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# Set to 1 if diploid leave empty otherwise
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diploid=
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## CONTACTS
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# Theta boundaries, from high to low
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thetas=(1 .2 .1 .05 .02 .01 0.001)
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# Molecular Dynamics configuration
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dconfFile="mflock.lua"
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## OPTIMIZATION
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nReassign=3
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outScript=chromflock_run
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touch $outScript
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chmod +x $outScript
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echo "" > $outScript
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##
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## RUN -- no need to edit below this line
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##
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# geostring goes into both aflock and mflock
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if [[ ! -z "$ea" ]]
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then
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geostring="--ea $ea --eb $eb --ec $ec"
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else
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geostring=
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fi
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# adiplo
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if [[ ! -z "$diploid" ]]
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then
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adiplo="--diploid"
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else
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adiplo=
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fi
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# For mflock
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moptstring="--cmmz $geostring --dconf $dconfFile"
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prArg=""
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if [[ ! -z "$rFile" ]]; then
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if [ -z "$prFile" ]
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then
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echo "rFile is set but not prFile. Same radial constraints for all structures."
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echo "Required action: Set kRad in mflock.lua"
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mflock_arguments="-r $rFile $moptstring -L $lFile"
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else
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# -r is set by aflock and put into mflock_jobs
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echo "rFile and prFile is set. Individual radial constraints for each structure"
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mflock_arguments="$moptstring -L $lFile"
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prArg="--rpos $rFile --prpos $prFile"
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fi
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else
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mflock_arguments="$moptstring -L $lFile"
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fi
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## Finialize the output script
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# One folder per structure will be created
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# and initialize with W from contacts
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# from A where theta == 1
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# A list of jobs to run will be written to `mflock_jobs`
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echo "set -e" >> $outScript
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echo echo ""Initialization started" > status.txt" >> $outScript
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echo "hostname >> status.txt" >> $outScript
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echo "aflock --version >> status.txt" >> $outScript
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echo "date >> status.txt" >> $outScript
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echo "aflock $adiplo $geostring -A $aFile -n $nStruct -I -Q $vq $prArg -P \""${mflock_arguments}\""" >> $outScript
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echo "date >> status.txt" >> $outScript
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echo "echo "Initialization done" >> status.txt" >> $outScript
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echo "echo "Running for theta==1"" >> $outScript
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# Run first batch of jobs in parallel
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echo "parallel --halt-on-error 2 --jobs $nCores --joblog parallel.log < mflock_jobs" >> $outScript
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nsteps=${#thetas[*]}
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if (( $nsteps > 1 )); then
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let "nsteps = $nsteps-1"
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# Then, for each theta value, run again (write as a loop)
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for idx in `seq 1 $nsteps`
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do
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thHigh=${thetas[$idx-1]}
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thLow=${thetas[$idx]}
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for iter in `seq 1 $nReassign`
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do
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echo "date >> status.txt" >> $outScript
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echo "echo "Assigning contacts where theta in [$thLow ,$thHigh ["" >> $outScript
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echo "aflock $adiplo $geostring -A $aFile $prArg -n $nStruct -Q $vq -h $thHigh -l $thLow -U" >> $outScript
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echo "date >> status.txt" >> $outScript
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echo "echo "Running for theta in [$thLow, $thHigh [" >> status.txt" >> $outScript
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echo "parallel --halt-on-error 2 --jobs $nCores --joblog parallel.log < mflock_jobs" >> $outScript
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echo "echo "ok" >> status.txt" >> $outScript
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done
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done
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fi
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echo "date >> status.txt" >> $outScript
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echo "echo "Finalizing ..." >> status.txt" >> $outScript
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echo "aflock $adiplo $geostring -F -A $aFile $prArg -n $nStruct -Q $vq" >> $outScript
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echo "date >> status.txt" >> $outScript
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echo "echo "Done!" >> status.txt" >> $outScript
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echo "Now run $outScript"

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