iteratively find one string and replace with corresponding value in table in bash: issue storing output to variables within a loop

Question

I am still new to coding and I am stuck!! I have a file with several hundred unique strings (names) that I would like to replace with unique new strings (useful names). I have the "old" names and "new" names in a csv file with each desired substitution on its own line. The target file to do the substituting is "testtree", which is just a text file. My goal is to come up with a solution that will iterate through each old/new pair and replace every old name with its respective new name in the "testtree" file. I would prefer to keep using bash.

sample_names.csv

myotis4703,M_yumanensis_TK4703
myotis4834,M_californicus_TK4834
myotis7111,M_sodalis_TK7111
myotis10123,M_nigricans_TK10123
myotis10319,M_albescens_TK10319
myotis13147,M_keaysi_TK13147

Here is what I have been trying:

cat sample_names.csv | while read i; do \
    OLD=$(echo ${i} | cut -d, -f1) \
    NEW=$(echo ${i} | cut -d, -f2) \
    sed -i 's/$OLD/$NEW/g' testtree; done

When I try to echo the OLD and NEW variables with this command:

cat sample_names.csv | while read i; do \
    OLD=$(echo ${i} | cut -d, -f1) \
    echo "The old name is" "$OLD"
    NEW=$(echo ${i} | cut -d, -f2) \
    echo "the new name is" "$NEW"; done

I get the following for every entry in my table (sample_names.csv):

The old name is 
the new name is

Clearly there is an issue with storing the cut output in the OLD and NEW variables. I have tried every combination I can think of of quotes, parentheses, etc., with no success. I would appreciate any suggestions! Thanks!

Your problem can be reduced to `foo=42 echo "foo is $foo"`. Nothing to do with loops or files. — melpomene, Sep 22 '18 at 16:58
Also, https://stackoverflow.com/questions/6697753/difference-between-single-and-double-quotes-in-bash. — melpomene, Sep 22 '18 at 17:09
Don't use the backslash at the end of your lines of code - doing so makes them a single command, and you don't want a single command. — linuxfan says Reinstate Monica, Sep 22 '18 at 17:12
This might help with GNU sed: `sed -i -f <(sed -E 's#(^|$|,)#/#g' sample_names.csv) testtree` — Cyrus, Sep 22 '18 at 17:17

score 0 · Answer 1 · answered Sep 23 '18 at 05:45

0

The mistake is the backslash \ of each line, removing these \

cat sample_names.csv | while read i; do
    OLD=$(echo ${i} | cut -d, -f1)
    echo "The old name is" "$OLD"
    NEW=$(echo ${i} | cut -d, -f2)
    echo "the new name is" "$NEW"; done

answered Sep 23 '18 at 05:45

Feng

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iteratively find one string and replace with corresponding value in table in bash: issue storing output to variables within a loop

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