bash script to iterate through folders - bash

Question

I have 5 folders in Test directory with name output001 to output005. Each output folders have files with filename *.cl_evt in it. I want to enter the each output folders and want to run the below command in bash shell script. How to iterate through each folder and run the below code through bash shell script ?
#!/bin/bash
echo -e "sw00092413002xpcw3po_cl.evt
sw00092413002xpcw3po_cl_bary4.evt
sw00092413002sao.fits.gz" | barycorr ra=253.467570 dec=39.760169

Answer 1

You can use the command seq (with a format) to generate the numbers in the name of your directories... Like that:
for i in $(seq -f "%03g" 1 5); do
cd output$i
echo -e "sw00092413002xpcw3po_cl.evt
sw00092413002xpcw3po_cl_bary4.evt
sw00092413002sao.fits.gz" | barycorr ra=253.467570 dec=39.760169
cd ..
done
If you want to adjust the name of the data file in each of the sub-directories, you can write it this way:
for i in $(seq -f "%03g" 1 5); do
cd output$i
f1=$(ls sw*pcw3po_cl.evt 2>/dev/null)
if [ "$f1" == "" ] ; then
echo "no data file in directory output$i"
continue
else
f2=${f1/pcw3po_cl.evt/pcw3po_cl_bary4.evt}
f3=$(ls sw*sao.fits.gz)
echo -e "$f1
$f2
$f3" | barycorr ra=253.467570 dec=39.760169
fi
cd ..
done
Break-down of the script:
the command :
seq -f "%03g" 1 5
generates the sequence:
001
002
003
004
005
Which means that the loop :
for i in $(seq -f "%03g" 1 5); do
will loop 5 times, with variable i successively taking the value 001, 002, 003, 004, 005
Inside each loop, we're running a few commands. (Let's analyse the first loop when i contains 001) :
the fist line of the loop :
cd output$i
is equivalent to output001 (so we go to the directory output001).
The last line of the loop:
cd ..
goes up one level in the directory tree (i.e. it returns to the directory where you were at the beginning of the script).
The following command executes : ls sw*pcw3po_cl.evt inside the directory output001 and puts the result in the variable f1 :
f1=$(ls sw*pcw3po_cl.evt)
The following command takes variable f1, substitutes the string pcw3po_cl.evt with pcw3po_cl_bary4.evt and puts the result in the variable f2 :
f2=${f1/pcw3po_cl.evt/pcw3po_cl_bary4.evt}
The following command executes : ls sw*sao.fits.gz inside the directory output001 and puts the result in the variable f3 :
f3=$(ls sw*sao.fits.gz)
The following command :
echo -e "$f1 $f2 $f3" | barycorr ra=253.467570 dec=39.760169
prints out the values of the 3 variables f1 f2 and f3 (which hopefully contains the file of the directory whose name matches (successively) swpcw3po_cl.evt, swpcw3po_cl_bary4.evt, and sw*sao.fits.gz
Then it "pipes" these values into your application named barycorr as standard input of this application (so barycorr can read these filenames and probably process the files).