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HybPhylomaker13_DiscoVista.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=24:0:0
#PBS -l select=1:ncpus=1:mem=4gb:scratch_local=4gb
#PBS -j oe
#PBS -N HybPhyloMaker13_DiscoVista
#PBS -m abe
#-------------------HYDRA-------------------
#$ -S /bin/bash
#$ -pe mthread 4
#$ -q sThM.q
#$ -l mres=4G,h_data=4G,h_vmem=4G,himem
#$ -cwd
#$ -j y
#$ -N HybPhyloMaker13_DiscoVista
#$ -o HybPhyloMaker13_DiscoVista.log
# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * https://github.com/tomas-fer/HybPhyloMaker *
# * Script 13 - DiscoVista *
# * v.1.8.1 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2021 *
# * [email protected] *
# ********************************************************************************
#Complete path and set configuration for selected location
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "\nHybPhyloMaker13 is running on MetaCentrum..."
#settings for MetaCentrum
#Move to scratch
cd $SCRATCHDIR
#Copy file with settings from home and set variables from settings.cfg
cp $PBS_O_WORKDIR/settings.cfg .
. settings.cfg
. /packages/run/modules-2.0/init/bash
path=/storage/$server/home/$LOGNAME/$data
source=/storage/$server/home/$LOGNAME/HybSeqSource
#Add necessary modules
module add R-3.4.3-gcc
module add python27-modules-gcc #adds also biopython and DendroPy
#module add debian8-compat
#Set package library for R
export R_LIBS="/storage/$server/home/$LOGNAME/Rpackages"
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "\nHybPhyloMaker13 is running on Hydra..."
#settings for Hydra
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir -p workdir13
cd workdir13
#Add necessary modules
module load tools/R/3.4.1
else
echo -e "\nHybPhyloMaker13 is running locally..."
#settings for local run
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir -p workdir13
cd workdir13
fi
#clone DiscoVista repository
git clone https://github.com/esayyari/DiscoVista
export WS_HOME=`pwd`
# R
# install.packages(c("reshape","reshape2","ggplot2","plyr","scales","ape","optparse"))
# pip install dendropy #Python2
#copy list of folders to compare
cp $source/comparelist.txt .
#method 0, 1, 5 (species tree)
mkdir species parameters genetrees rel_frequency
#copy annotations
cp $source/annotation.txt parameters/
#create clade-defs.txt file
$WS_HOME/DiscoVista/src/utils/generate_clade-defs.py parameters/annotation.txt parameters/clade-defs.txt
#copy species trees defined in 'comparelist.txt' to respective folders
for i in $(cat comparelist.txt); do
if [ ! -z $(grep exon <<< $i) ]; then ty=exon; fi
if [ ! -z $(grep cp <<< $i) ]; then ty=cp; fi
if [ ! -z $(grep corrected <<< $i) ]; then corr=corr; else corr=orig; fi
if [ ! -z $(grep RAxML <<< $i) ]; then tr=RAxML; fi
if [ ! -z $(grep FastTree <<< $i) ]; then tr=FastTree; fi
if [ ! -z $(grep update <<< $i) ]; then up=update; else up=all; fi
if [ ! -z $(grep collapsed <<< $i) ]; then col=$(tr '/' '\n' <<< $i | grep collapsed); else col=nocol; fi
if [ $(tr '/' '\n' <<< $i | sed "s/_corrected/_corrected\n/" | sed 's/species_trees//' | tr '_' '\n' | sed '/^$/d' | grep trees -n | cut -d ':' -f 1) -eq 2 ]; then sl=nosel; fi
if [ $(tr '/' '\n' <<< $i | sed "s/_corrected/_corrected\n/" | sed 's/species_trees//' | tr '_' '\n' | sed '/^$/d' | grep trees -n | cut -d ':' -f 1) -eq 3 ]; then sl=$(tr '/' '\n' <<< $i | sed '/^$/d' | sed -n 2p); fi
mis=$(tr '/' '\n' <<< $i | grep [0-9]tree | sed 's/82trees_corrected//' | sed 's/72trees//' | cut -d '_' -f 1)
pres=$(tr '/' '\n' <<< $i | grep [0-9]tree | sed 's/82trees_corrected//' | sed 's/72trees//' | cut -d '_' -f 2)
if [ ! -z $(grep Astral <<< $i) ]; then str=Astral; fi
if [ ! -z $(grep Astrid <<< $i) ]; then str=Astrid; fi
if [ ! -z $(grep MRL <<< $i) ]; then str=MRL; fi
if [ ! -z $(grep "concatenated$" <<< $i) ]; then str=concatFT; fi
if [ ! -z $(grep concatenatedExaML <<< $i) ]; then str=concatExaML; fi
dirn=${str}.${ty}.${mis}.${pres}.${corr}.${sl}.${tr}.${up}.${col}
mkdir species/$dirn
mkdir genetrees/$dirn
mkdir rel_frequency/$dirn
# fix i to not contain SPECIENSTREE FOLDER
speciestree_folder=$(sed 's![^/]*$!!' <<< ${i})
cp ${path}${speciestree_folder}/trees.newick genetrees/$dirn/genetrees.tree
sed -i 's/-/_/g' genetrees/$dirn/genetrees.tree #replace all '-' occurrences by '-'
cp ${path}${speciestree_folder}/trees.newick rel_frequency/$dirn/estimated_gene_trees.tree
sed -i 's/-/_/g' rel_frequency/$dirn/estimated_gene_trees.tree #replace all '-' occurrences by '-'
#check for Astral
if [ ! -z $(grep Astral <<< $i) ]; then
if [[ $col =~ "nocol" ]]; then
cp ${path}${i}/Astral_${mis}_${pres}.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/Astral_${mis}_${pres}.tre rel_frequency/$dirn/estimated_species_tree.tree
else
cp ${path}${i}/Astral_${mis}_${pres}_${col}.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/Astral_${mis}_${pres}_${col}.tre rel_frequency/$dirn/estimated_species_tree.tree
fi
sed -i 's/ /_/g' species/$dirn/estimated_species_tree.tree #replace all ' ' occurrences by '-'
fi
#check for Astrid
if [ ! -z $(grep Astrid <<< $i) ]; then
if [[ $col =~ "nocol" ]]; then
cp ${path}${i}/Astrid_${mis}_${pres}.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/Astrid_${mis}_${pres}.tre rel_frequency/$dirn/estimated_species_tree.tree
else
cp ${path}${i}/Astrid_${mis}_${pres}_${col}.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/Astrid_${mis}_${pres}_${col}.tre rel_frequency/$dirn/estimated_species_tree.tree
fi
sed -i 's/ /_/g' species/$dirn/estimated_species_tree.tree #replace all ' ' occurrences by '-'
fi
#check for MRL
if [ ! -z $(grep MRL <<< $i) ]; then
if [[ $col =~ "nocol" ]]; then
cp ${path}${i}/MRL_${mis}_${pres}.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/MRL_${mis}_${pres}.tre rel_frequency/$dirn/estimated_species_tree.tree
else
cp ${path}${i}/MRL_${mis}_${pres}_${col}.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/MRL_${mis}_${pres}_${col}.tre rel_frequency/$dirn/estimated_species_tree.tree
fi
sed -i 's/ /_/g' species/$dirn/estimated_species_tree.tree #replace all ' ' occurrences by '-'
fi
#check for concatenated
if [ ! -z $(grep "concatenated$" <<< $i) ]; then
if [[ $col =~ "nocol" ]]; then
cp ${path}${i}/concatenated${mis}_${pres}.fast.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/concatenated${mis}_${pres}.fast.tre rel_frequency/$dirn/estimated_species_tree.tree
else
cp ${path}${i}/concatenated${mis}_${pres}_${col}.fast.tre species/$dirn/estimated_species_tree.tree
cp ${path}${i}/concatenated${mis}_${pres}_${col}.fast.tre rel_frequency/$dirn/estimated_species_tree.tree
fi
sed -i 's/ /_/g' species/$dirn/estimated_species_tree.tree #replace all ' ' occurrences by '-'
fi
#check for concatenatedExaML
if [ ! -z $(grep concatenatedExaML <<< $i) ]; then
if [[ $col =~ "nocol" ]]; then
cp ${path}${i}/ExaML_bootstrap_${mis}_${pres}.tre species/$dirn/estimated_species_tree.tree
else
cp ${path}${i}/ExaML_bootstrap_${mis}_${pres}_${col}.tre species/$dirn/estimated_species_tree.tree
fi
fi
sed -i 's/ /_/g' species/$dirn/estimated_species_tree.tree #replace all ' ' occurrences by '-'
sed -i 's/ /_/g' rel_frequency/$dirn/estimated_species_tree.tree #replace all ' ' occurrences by '-'
# prepare data for m1
# write each gene tree to single file
mkdir -p genetrees/input
num=1
while read line
do
mkdir -p genetrees/input/tree_${num}
mkdir genetrees/input/tree_${num}/${dirn}
echo "$line" > genetrees/input/tree_${num}/${dirn}/estimated_gene_trees.tree
let num=num+1
done < genetrees/$dirn/genetrees.tree
# run m5
mkdir rel_frequency/$dirn/results
#Run DiscoVista M5
$WS_HOME/DiscoVista/src/utils/discoVista.py -c parameters/clade-defs.txt -p rel_frequency/$dirn/ -t 90 -m 5 -o rel_frequency/$dirn/results -a parameters/annotation.txt -g Outgroup
done
#Run DiscoVista M0
$WS_HOME/DiscoVista/src/utils/discoVista.py -c parameters/clade-defs.txt -p species/ -t 0.90 -m 0 -o results
#Run DiscoVista M1
$WS_HOME/DiscoVista/src/utils/discoVista.py -c parameters/clade-defs.txt -p genetrees/input/ -t 90 -m 1 -o genetrees/results -a parameters/annotation.txt -k 20
#Make dir for results
mkdir -p $path/DiscoVista/speciestree
#Copy results back to home
cp -r species/ $path/DiscoVista/speciestree
cp -r parameters/ $path/DiscoVista/speciestree
cp -r results/ $path/DiscoVista/speciestree
cp comparelist.txt $path/DiscoVista/speciestree
p -r genetrees/ $path/DiscoVista/
cp comparelist.txt $path/DiscoVista/genetrees
cp -r parameters/ $path/DiscoVista/genetrees
cp -r rel_frequency/ $path/DiscoVista/
cp -r parameters/ $path/DiscoVista/rel_frequency
cp comparelist.txt $path/DiscoVista/rel_frequency
#Clean scratch/work directory
if [[ $PBS_O_HOST == *".cz" ]]; then
#delete scratch
if [[ ! $SCRATCHDIR == "" ]]; then
rm -rf $SCRATCHDIR/*
fi
else
cd ..
rm -r workdir13
fi
echo -e "\nScript HybPhyloMaker13 finished...\n"