Element matching within the different lists - bash

Question

As usually :) I have two sets of input files with the same names but different extensions.
Using bash I made simple script which create 2 lists with identical elements names while looping 2 sets of the files from 2 dirs and using only it names w/o extensions as the elements of those lists:
#!/bin/bash
workdir=/data2/Gleb/TEST/claire+7d4+md/water_analysis/MD1
traj_all=${workdir}/tr_all
top_all=${workdir}/top_all
#make 2 lists for both file types
Trajectories=('');
Topologies=('');
#looping of 1st input files
echo "Trr has been found in ${traj_all}:"
for tr in ${traj_all}/*; do # ????
tr_n_full=$(basename "${tr}")
tr_n="${tr_n_full%.*}"
Trajectories=("${Trajectories[#]}" "${tr_n}");
done
#sort elements within ${Trajectories[#]} lists!! >> HERE I NEED HELP!
#looping of 2nd files
echo "Top has been found in ${top_all}:"
for top in ${top_all}/*; do # ????
top_n_full=$(basename "${top}")
top_n="${top_n_full%.*}"
Topologies=("${Topologies[#]}" "${top_n}");
done
#sort elements within ${Topologies[#] lists!! >> HERE I NEED HELP!
#make input.in file for some program- matching of elements from both lists >> HERE I NEED HELP!
for i in $(seq 1 ${#Topologies[#]}); do
printf "parm $top_all/${Topologies[i]}.top \ntrajin $traj_all/${Trajectories[i]}.mdcrd\nwatershell ${Area} ${output}/watershell_${Topologies[i]}_${Area}.dat > output.in
done
I'd thankful if someone provide me with good possibility how to improve this script:
1) I need to sort elements in both lists in the similar pattern after last elements have been added in each of them;
2) I need to add some test on the LAST step of the script which will create final output.in file only in case if elements are the same (in principle in this case it always should be the same!) in both lists which are matched during this operation by printf.
Thanks for the help,
Gleb

Answer 1

Here's a simpler way to create the arrays:
# Create an empty array
Trajectories=();
for tr in "${traj_all}"/*; do
# Remove the string of directories
tr_base=${tr##*/}
# Append the name without extension to the array
Trajectories+="${tr_base%.*}"
done
In bash, this will normally result in a sorted list, because the expansion of * in the glob is sorted. But you can sort it with sort; it is simplest if you are certain there are no newlines in the filenames:
mapfile -t sorted_traj < <(printf %s\\n "${Trajectories[#]}" | sort)
To compare two sorted arrays, you could use join:
# convenience function; could have helped above, too.
lines() { printf %s\\n "$#"; }
# Some examples:
# 1. compare a with b and print the lines which are only in a
join -v 1 -t '' <(lines "${a[#]}") <(lines "${b[#]}")
# 2. create c as an array with the lines which are only in b
mapfile -t c < <( join -v 2 -t '' <(lines "${a[#]}") <(lines "${b[#]}") )
If you create both difference lists, then the two arrays are equal if both lists are empty. If you are expecting both arrays to be the same, though, and if this is time-critical (probably not), you could do a simple precheck:
if [[ "${a[*]}" = "${b[*]}" ]]; then
# the arrays are the same
else
# the arrays differ; do some more work to see how.
fi