TriTrypGenome/generateLogos.sh at master · fhadinezhadUC/TriTrypGenome · GitHub

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#!/bin/bash
# this script will run tsfm on all the genomes
# for each genomes it will make a folder in each folder will make three folders: KLD,ID,Func, bubble_Table


folderpath=$(pwd) #"/home/fatemeh/Leishmania_2019/Leishmania_2019/Results/tsfminput_final/input3/"
tsfmpath="/home/fatemeh/Leishmania_Aug2018/phyloclassification/tsfm-master/tsfm"
folders=$(ls -l $folderpath | grep "^d" | awk -F" " '{print $9}')

# creating function logos
#for name1 in $folders; do
#if [ $name1 != "Logos" ]
#then
#printf "***************$name1***************"
#	mkdir -p "$folderpath/Logos/$name1/KLD"
#	mkdir -p "$folderpath/Logos/$name1/ID"
#	mkdir -p "$folderpath/Logos/$name1/Func"
#	mkdir -p "$folderpath/Logos/$name1/Bubble"
#run tsfm to make the logos
#name2=${name1%".v5"}
#name3="$name2.sites72.v5"
#printf "$name3"
#python3 "$tsfmpath/tsfm.py" -c "$folderpath/tsfm_finalinput_HomoC_structfile.txt" --logo "$folderpath/$name1/$name3"
#mv -- *.eps "$folderpath/Logos/$name1/Func"
#fi
#done
# creating ID, KLD, and tables for the bubble plots
for name1 in $folders; do
if [ $name1 != "Logos" ]
then
printf "***************$name***************"
name2=${name1%".v5"}
name3="$name2.sites72.v5"

python3 "$tsfmpath/tsfm.py" -c "$folderpath/tsfm_finalinput_HomoC_structfile.txt" --idlogo "$folderpath/$name1/$name3" "$folderpath/HOMO.v5/HOMO.sites72.v5"
mv -- *.eps "$folderpath/Logos/$name1/ID"

#python3 "$tsfmpath/tsfm.py" -c "$folderpath/tsfm_finalinput_HomoC_structfile.txt" --kldlogo "$folderpath/$name1/$name3" "$folderpath/HOMO.v5/HOMO.sites72.v5"
#mv -- *.eps "$folderpath/Logos/$name1/KLD"

python3 "$tsfmpath/tsfm.py" -c "$folderpath/tsfm_finalinput_HomoC_structfile.txt" --bt "$folderpath/$name1/$name3" "$folderpath/HOMO.v5/HOMO.sites72.v5"
rm -- *.eps

mv *_Table.txt "$folderpath/Logos/$name1/Bubble"
fi
done