rename_remove.sh

#!/bin/bash

#Script for renaming species in 1_data based on names_1_data_rename_seqs.csv

# Loading commandline data
while getopts r:d: flag
do
	case "${flag}" in
		r) rename_file=${OPTARG};;
		d) remove_file=${OPTARG};;
	esac
done

# Check if rename file is provided
if [ -z "$rename_file" ]; then
	echo "Please provide a rename file using the -r option."
	exit 1
fi

# Check if remove file is provided
if [ -z "$remove_file" ]; then
	echo "Please provide a remove file using the -d option."
	exit 1
fi

# Removing unnecessary files 
rm *.xml *.csv

# Unpacking zip files
gunzip *gz

# Copying renaming list into folder
cp "$rename_file" .

# Renaming the files
cat "$rename_file" | while IFS=, read orig new; do mv "$orig" "$new"; done

# Removing the renaming list
rm "$rename_file"

# Removing hidden characters which were created by the renaming script
for f in *; do echo mv "$f" "$(sed 's/[^0-9A-Za-z_.]/_/g' <<< "$f")"; done

rename -n 's/(.*).{1}/$1/' *

# Removing files with bad clean in name
rm *.clean_*

# Removing files specified in the remove file
for f in $(cat "$remove_file")
do
	rm "$f"
done

# Removing leftover shell scripts within data folder
rm *.sh

# #Removing unnecessary files 
# rm *.xml *.csv

# #Unpacking zip files
# gunzip *gz

# #Copying renaming list into folder
# cp /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/names_1_data_1_rename_seqs.csv .

# #Renaming the files
# cat names_1_data_1_rename_seqs.csv | while IFS=, read orig new; do mv "$orig" "$new"; done

# #Removing the renaming list
# rm names_1_data_1_rename_seqs.csv

# #Removing hidden characters which were created by the renaming script
# for f in *; do echo mv "$f" "$(sed 's/[^0-9A-Za-z_.]/_/g' <<< "$f")"; done

# rename -n 's/(.*).{1}/$1/' *

# # Removing files with bad clean in name
# rm *.clean_*

# # Removing files with in names_1_data_2_rm_seqs.csv
# for f in $(cat /home/owrisberg/Coryphoideae/github_code/coryphoideae_species_tree/names_1_data_2_rm_seqs.csv)
# do
# rm "$f"
# done

# #Removing leftover shell scripts within datafolder 
# rm *.sh