How to come in only in the new directory with script bash - bash

Question

#!/bin/bash
#cicle 1
for fname in *.xlsx *csv
do
dname=${fname%.*}
[[ -d $dname ]] || mkdir "$dname"
mv "$fname" "$dname"
done
# In questo ciclo per ogni gene entra nella cartella e lancia i programmi di getChromosomicPositions.sh per avere
# le posizioni nel genoma, e getHapolotipeStings.sh per avere le varianti
#cicle 2
for geni in */; do
cd $geni
z=$(tail -n 1 *.csv | tr ';' "\n" | wc -l) # geuarda nel file csv quante colonne ci sono e trasferisce il riusltato al programma getChromosomicPositions
cd ..
cp getHGSVposHG19.sh $geni
cp getChromosomicPositions.sh $geni
cp getHaplotypeStrings.sh $geni
cd $geni
pippo=$(basename $(pwd))
export z
export pippo
./getChromosomicPositions.sh *.csv
export z
./getHaplotypeStrings.sh *.csv
cd ..
done
I have this script with 2 cicle,
I want that at the cicle 2 do the work of compilate the programs only for the new directory created in the cicle 1.
I mean:
I have the principal directory with this file:
pippo.xlsx pippo.csv
caio.xlsx caio.csv
topolino(directory)
minny(directory)
paperino(directory)
in the cicle 1 make the directorys pippo and caio
I want that at the cicle 2 I want that comes in in the new directory (pippo, caio) and makes all the work of cicle only to the new directory pippo and caio but not to the old directorys topolino, minny and paperino.
How can I do this?

Answer 1

You could create an array with the newly created directories, and then loop over this array:
#!/bin/bash
set -o errexit # Exit the script in case of error
# Pre-declare and empty array.
declare -a new_directories;
# Save other scripts path for later use.
getHGSVposHG19="${pwd}/getHGSVposHG19.sh"
getChromosomicPositions="${pwd}/getChromosomicPositions.sh"
getHaplotypeStrings="${pwd}/getHaplotypeStrings.sh"
# Create missing directories
for fname in *.xlsx *csv
do
dname=${fname%.*}
if [ ! -d $dname ]
then
mkdir "$dname";
new_directories+=("${dname}");
fi
mv "$fname" "$dname";
done
# Initialize only new directories
for geni in "${new_directories[#]}"
do
pushd "${geni}"; # Add to directory stack
export pippo="$(basename $(pwd))";
export z=$(tail -n 1 *.csv | tr ';' "\n" | wc -l)
"${getChromosomicPositions}" *.csv;
export z; # Is the previous script modifying z?
"${getHaplotypeStrings}" *.csv;
popd; #Remove from directory stack
done
I also took the liberty to clean your script a bit, since I can't run it as is, it might have some typos/bugs...
What is pushd and popd?