Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add -m 1 and -m 5 #15

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Add -m 1 and -m 5 #15

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
65 changes: 58 additions & 7 deletions HybPhylomaker13_DiscoVista.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=24:0:0
#PBS -l select=1:ncpus=4:mem=16gb:scratch_local=4gb
#PBS -l select=1:ncpus=1:mem=4gb:scratch_local=4gb
#PBS -j oe
#PBS -N HybPhyloMaker13_DiscoVista
#PBS -m abe
Expand All @@ -19,7 +19,7 @@
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * https://github.com/tomas-fer/HybPhyloMaker *
# * Script 13 - DiscoVista *
# * v.1.8.0b *
# * v.1.8.1 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2021 *
# * [email protected] *
# ********************************************************************************
Expand Down Expand Up @@ -77,8 +77,8 @@ export WS_HOME=`pwd`
#copy list of folders to compare
cp $source/comparelist.txt .

#method 1 (species tree)
mkdir species parameters
#method 0, 1, 5 (species tree)
mkdir species parameters genetrees rel_frequency
#copy annotations
cp $source/annotation.txt parameters/
#create clade-defs.txt file
Expand All @@ -102,41 +102,61 @@ for i in $(cat comparelist.txt); do
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}-FNA
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
Expand All @@ -148,10 +168,33 @@ for i in $(cat comparelist.txt); do
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
$WS_HOME/DiscoVista/src/utils/discoVista.py -c parameters/clade-defs.txt -p species/ -t 0.95 -m 0 -o results
#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
Expand All @@ -161,6 +204,14 @@ 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
Expand Down