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HybPhyloMaker10_requisite_collapse.sh
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HybPhyloMaker10_requisite_collapse.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=1:0:0
#PBS -l select=1:ncpus=1:mem=1gb:scratch_local=1gb
#PBS -j oe
#PBS -N HybPhyloMaker10_requisite_collapse
#PBS -m abe
#-------------------HYDRA-------------------
#$ -S /bin/bash
#$ -q sThC.q
#$ -l mres=1G
#$ -cwd
#$ -j y
#$ -N HybPhyloMaker10_requisite_collapse
#$ -o HybPhyloMaker10_requisite_collapse.log
# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * https://github.com/tomas-fer/HybPhyloMaker *
# * Script 10 - Select trees with requisite taxa, collapse unsupported branches *
# * v.1.8.0a *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2021 *
# * tomas.fer@natur.cuni.cz *
# ********************************************************************************
#Select only gene trees and selected loci containing 'requisite' samples
#If requested, also collapse unsupported branches in gene trees (according to 'collapse' in settings.cfg) using TreeCollapseCL4.jar
#Produces
# - a NEWICK file only with trees containing requisite samples (trees_with_requisite.newick)
# - a text file with alignment file names containing requisite samples (selected_genes_with_requisite.txt)
# - a NEWICK file with trees with unsupported branches collapsed (trees_with_requisite_collapsed${collapse}.newick)
#Complete path and set configuration for selected location
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "\nHybPhyloMaker10_requisite_collapse 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 jdk-1.6.0
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "\nHybPhyloMaker10_requisite_collapse is running on Hydra..."
#settings for Hydra
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir -p workdir10
cd workdir10
#Add necessary modules
module load java/1.7
else
echo -e "\nHybPhyloMaker10_requisite_collapse 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 workdir10
cd workdir10
fi
#Setting for the case when working with cpDNA
if [[ $cp =~ "yes" ]]; then
echo -en "Working with cpDNA"
type="cp"
else
echo -en "Working with exons"
type="exons"
fi
#Settings for selection and (un)corrected reading frame
if [ -z "$selection" ]; then
if [[ $corrected =~ "yes" ]]; then
mafftpath=$type/61mafft_corrected
alnpath=$type/80concatenated_exon_alignments_corrected
alnpathselected=$type/81selected_corrected
treepath=$type/82trees_corrected
echo -e "...with corrected reading frame"
else
mafftpath=$type/60mafft
alnpath=$type/70concatenated_exon_alignments
alnpathselected=$type/71selected
treepath=$type/72trees
echo -e ""
fi
else
if [[ $corrected =~ "yes" ]]; then
mafftpath=$type/$selection/61mafft_corrected
alnpath=$type/$selection/80concatenated_exon_alignments_corrected
alnpathselected=$type/$selection/81selected_corrected
treepath=$type/$selection/82trees_corrected
echo -e "...with corrected reading frame...and for selection: $selection"
else
mafftpath=$type/$selection/60mafft
alnpath=$type/$selection/70concatenated_exon_alignments
alnpathselected=$type/$selection/71selected
treepath=$type/$selection/72trees
echo -e "...and for selection: $selection"
fi
fi
if [[ $update =~ "yes" ]]; then
echo -e "...and with updated gene selection"
else
if [[ $requisite =~ "no" ]]; then
echo -e ""
fi
fi
if [[ $requisite =~ "yes" ]]; then
echo -e "...and only with trees with requisite taxa present\n"
else
echo -e "\n"
fi
if [[ ! $location == "1" ]]; then
if [ "$(ls -A ../workdir10)" ]; then
echo -e "Directory 'workdir10' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
rm -d ../workdir10 2>/dev/null
exit 3
fi
fi
#Write log
logname=HPM10
echo -e "HybPhyloMaker10: select trees with requisite taxa, collapse unsupported branches" > ${logname}.log
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "run on MetaCentrum: $PBS_O_HOST" >> ${logname}.log
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "run on Hydra: $HOSTNAME" >> ${logname}.log
else
echo -e "local run: "`hostname`"/"`whoami` >> ${logname}.log
fi
echo -e "\nBegin:" `date '+%A %d-%m-%Y %X'` >> ${logname}.log
echo -e "\nSettings" >> ${logname}.log
if [[ $PBS_O_HOST == *".cz" ]]; then
printf "%-25s %s\n" `echo -e "\nServer:\t$server"` >> ${logname}.log
fi
for set in data selection cp corrected update MISSINGPERCENT SPECIESPRESENCE tree OUTGROUP collapse requisite requisitetaxa; do
printf "%-25s %s\n" `echo -e "${set}:\t" ${!set}` >> ${logname}.log
done
if [[ $requisite =~ "yes" ]]; then
echo -e "\nList of requisite samples" >> ${logname}.log
echo $requisitetaxa | tr '|' '\n' >> ${logname}.log
fi
if [ ! -z "$selection" ]; then
echo -e "\nList of excluded samples" >> ${logname}.log
cat $source/excludelist.txt >> ${logname}.log
echo >> ${logname}.log
fi
#Add necessary programs and files
cp $source/TreeCollapseCL4.jar .
if [[ $requisite =~ "no" ]] && [[ $collapse -eq "0" ]]; then
echo "Nothing to do..."
fi
#Copy genetree file
if [[ $requisite =~ "yes" ]]; then
if [[ $update =~ "yes" ]]; then
if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/trees_rooted_with_requisite.newick" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/trees_rooted_with_requisite.newick .
else
if [ -z "$OUTGROUP" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees.newick .
mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite
mv trees.newick trees_rooted.newick
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees_rooted.newick .
mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite
fi
fi
else
if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/trees_rooted_with_requisite.newick" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/trees_rooted_with_requisite.newick .
else
if [ -z "$OUTGROUP" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees.newick .
mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite
mv trees.newick trees_rooted.newick
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees_rooted.newick .
mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite
fi
fi
fi
else
if [[ $update =~ "yes" ]]; then
if [ -z "$OUTGROUP" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees.newick .
mv trees.newick trees_rooted.newick
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees_rooted.newick .
fi
else
if [ -z "$OUTGROUP" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees.newick .
mv trees.newick trees_rooted.newick
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees_rooted.newick .
fi
fi
fi
#Select only trees with requisite taxa and copy the file to home
if [[ $requisite =~ "yes" ]]; then
if [ ! -f "trees_rooted_with_requisite.newick" ]; then
echo -e "Selecting trees with requisite taxa..."
grep -E "$requisitetaxa" trees_rooted.newick > trees_rooted_with_requisite.newick
#Copy selected trees to home
if [[ $update =~ "yes" ]]; then
if [ -z "$OUTGROUP" ]; then
cp trees_rooted_with_requisite.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/trees_with_requisite.newick
else
cp trees_rooted_with_requisite.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite
fi
else
if [ -z "$OUTGROUP" ]; then
cp trees_rooted_with_requisite.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/trees_with_requisite.newick
else
cp trees_rooted_with_requisite.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite
fi
fi
fi
fi
#Make a list of genes containing requisite taxa in alignment
if [[ $requisite =~ "yes" ]]; then
echo -e "Preparing list of genes containing requisite taxa..."
#grep only filenames of alignments (option '-l') containing requisite taxa (sed command extract only filenames without extension from the full path)
grep -El "$requisitetaxa" $path/${alnpathselected}${MISSINGPERCENT}/deleted_above${MISSINGPERCENT}/*modif* | sed -r "s/.+\/(.+)\..+/\1/" > genes_with_requisite_ALL.txt
if [[ $update =~ "yes" ]]; then
#Copy list of selected genes
cp $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt .
#Add '_' before and after each numbers
awk '{ print "_" $0 "_" }' selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt > tmp && mv tmp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt
#Take only selected genes with requisite taxa
grep -F -f selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt < genes_with_requisite_ALL.txt > selected_genes_with_requisite.txt
cut -d'_' -f2 selected_genes_with_requisite.txt > tmp && mv tmp selected_genes_with_requisite.txt
cp selected_genes_with_requisite.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite
else
#Copy list of selected genes
cp $path/${alnpathselected}${MISSINGPERCENT}/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt .
#Take only numbers of selected genes
cut -d'_' -f2 selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt > tmp && mv tmp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt
#Add '_' before and after each numbers
awk '{ print "_" $0 "_" }' selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt > tmp && mv tmp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt
#Take only selected genes with requisite taxa
grep -F -f selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}.txt < genes_with_requisite_ALL.txt > selected_genes_with_requisite.txt
cut -d'_' -f2 selected_genes_with_requisite.txt > tmp && mv tmp selected_genes_with_requisite.txt
cp selected_genes_with_requisite.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite
fi
fi
#Collapse trees using 'TreeCollapseCL4'
if [[ ! $collapse -eq "0" ]]; then
echo -e "Collapsing tree branches with BS below ${collapse}..."
unset i
mkdir trees
#Put all trees one-by-one to folder 'tree'
if [[ $requisite =~ "yes" ]]; then
for x in $(<trees_rooted_with_requisite.newick); do
echo "$x" > trees/tree$((++i)).tre
done
if [[ $location == "2" ]]; then
java -d64 -server -XX:MaxHeapSize=1g -jar TreeCollapseCL4.jar -b ${collapse} -d trees/ 1>/dev/null
else
java -jar TreeCollapseCL4.jar -b ${collapse} -d trees/ 1>/dev/null
fi
cat trees/*coll* > trees_with_requisite_collapsed${collapse}.newick
if [[ $update =~ "yes" ]]; then
mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/collapsed${collapse}
cp trees_with_requisite_collapsed${collapse}.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/collapsed${collapse}
else
mkdir -p $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/collapsed${collapse}
cp trees_with_requisite_collapsed${collapse}.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/collapsed${collapse}
fi
else
for x in $(<trees_rooted.newick); do
echo "$x" > trees/tree$((++i)).tre
done
if [[ $location == "2" ]]; then
java -d64 -server -XX:MaxHeapSize=1g -jar TreeCollapseCL4.jar -b ${collapse} -d trees/ 1>/dev/null
else
java -jar TreeCollapseCL4.jar -b ${collapse} -d trees/ 1>/dev/null
fi
cat trees/*coll* > trees_collapsed${collapse}.newick
if [[ $update =~ "yes" ]]; then
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/collapsed${collapse}
cp trees_collapsed${collapse}.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/collapsed${collapse}
else
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/collapsed${collapse}
cp trees_collapsed${collapse}.newick $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/collapsed${collapse}
fi
fi
fi
#Copy log to home
echo -e "\nEnd:" `date '+%A %d-%m-%Y %X'` >> ${logname}.log
if [[ ! $collapse -eq "0" ]]; then
if [[ $requisite =~ "yes" ]]; then
if [[ $update =~ "yes" ]]; then
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/collapsed${collapse}
else
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/collapsed${collapse}
fi
else
if [[ $update =~ "yes" ]]; then
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/collapsed${collapse}
else
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/collapsed${collapse}
fi
fi
else
if [[ $requisite =~ "yes" ]]; then
if [[ $update =~ "yes" ]]; then
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite
else
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite
fi
fi
fi
#Clean scratch/work directory
if [[ $PBS_O_HOST == *".cz" ]]; then
#delete scratch
if [[ ! $SCRATCHDIR == "" ]]; then
rm -rf $SCRATCHDIR/*
fi
else
cd ..
rm -r workdir10
fi
echo -e "\nScript HybPhyloMaker10_requisite_collapse finished...\n"