Shell Programming and Scripting

#!/bin/bash

# enter name
printf "What is the name of the panel (please use CAPS): "; read name

# enter gene input
printf "%s \n" "Please enter gene(s), use a comma between multiple:" ; IFS="," read -a genes
for (( i = 0; i < ${#genes[@]}; i++ ))
do
    printf "%s\n" "${genes[$i]}" > /home/cmccabe/Desktop/NGS/panels/new.txt
    # remove line endings and trim
     sed 's/\r$//' < /home/cmccabe/Desktop/NGS/panels/new.txt | sed 's/^[ \t]*//;s/[ \t]*$//' > /home/cmccabe/Desktop/NGS/panels/${name}_unix_trim.bed
done

# create total target length for input
awk 'NR==FNR{A[$1];next}$1 in A' /home/cmccabe/Desktop/NGS/panels/${name}_unix_trim.bed /home/cmccabe/Desktop/NGS/bed/bedtools/IDP_total_target_length_by_panel/IDP_unix_trim_total_target_length.bed > /home/cmccabe/Desktop/NGS/bed/bedtools/IDP_total_target_length_by_panel/${name}_unix_trim_total_target_length.bed

#-------------------------------------------------------------------------#
# convert name to lower case
y="$name"
val=$(echo "$y" | tr '[:upper:]' '[:lower:]')
string="$val"

echo "This is the new panel to add" $string

# create function
printf "$string() {"
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