Extracting SST time series at multiple lat, lon locations using CDO - cdo-climate

Question

Background: I am working with satellite observations of SST (time, lat, lon) from the CoRTAD SST dataset (netCDF file). I have a set of (lon,lat) coordinates following the coastal contour of Portugal (called below midshelf locations). I want to extract the SST time series at each of these midshelf locations, average them and subtract the SST at the same latitudes but a fixed longitude to give a coastal SST index.
The midshelf lon,lats were determined first from a nautical chart, which were then linearly interpolated to the lon,lats in the CoRTAD grid.
How can this be done using CDO?
The lon,lats from the nautical map are given below.
midshelf lon,lats from the nautical map:
-8.000 43.860
-9.000 43.420
-9.350 43.220
-9.388 42.893
-9.000 42.067
-8.935 41.308
-9.000 40.692
-9.278 40.000
-9.324 39.550
-9.518 39.387
-9.777 38.883
-9.285 38.378
-8.909 38.293
-8.951 38.000
-8.965 37.953
-8.917 37.833
-8.913 37.667
-8.915 37.500
-8.975 37.333
-9.017 37.167
-9.045 37.000

Answer 1

So here is my attempt to answer the question as it was stated in the comments (i.e. you wanted an index which was the midshelf locations averaged and then subtracting the same latitude SST sampled at Longitude=9E). I assume the locations are stored pair-wise in a text file called "locations.txt" as in your question above. The loop part of the answer is from one of this question's solutions.
# first loop over the pairs of indices in the text files.
while read -r -a fields; do
for ((i=0; i < ${#fields[#]}; i += 2)); do
# precise lon/lat for sampled mid-shelf
cdo remapnn,"lon=${fields[i]}/lat=${fields[i+1]}" in.nc pt_${i}.nc
# same lat but lon=9E (change as wanted)
cdo remapnn,"lon=9/lat=${fields[i+1]}" in.nc 9E_${i}.nc
done
done < example.txt
# now take the ensemble average over the points.
cdo ensmean pt_*.nc mid_shelf_sst.nc
cdo ensmean 9E_*.nc mid_shelf_9E.nc
# and calculate the index
cdo sub mid_shelf_sst.nc mid_shelf_9E.nc SST_index.nc