Performing Prime Key function using 'Sed' in Bash

Question

I am using bash and trying to employ sed command for matching a string and replace it with another between two files.

Objective: To replace all strings[sp_*] by matching them from another file containing [sp_* Var_Names]. Please be noted that: 1. The order is synchronized but not consecutive in both files, so cannot use paste. 2. Functionality is similar to primeKey operations in mysql.

---

File 1

+--sp_O00574_
|
+--sp_Q9TV16_
|
|     +--sp_O18983_
|  +--| (52)
|  |  |  +--sp_Q9BDS6_
|  |  +--| (26)
|  |     |  +--sp_O19024_
|  |     +--| (29)
|  |        +--sp_Q9XT45_

---

File2

O00574  CXCR6_HUMAN
Q9TV16  CXCR6_PANTR
O18983  CXCR6_CHLAE
Q9BDS6  CXCR6_MACFA
O19024  CXCR6_MACNE
Q9XT45  CXCR6_MACMU

---

Purpose: To sed -ie 's/O00574/CXCR6_HUMAN/g' File1

inline Bash script:

cat File2 | while read id; do upID=`echo $id | cut -d " " -f1`; upName=`echo $id | cut -d " " -f2`; sed -ie 's/sp_$upID/$upName/g' File1; done

Script.sh

#/bin/bash

cat File2 | while read id;
do
    upID=`echo $id | cut -d " " -f1`
    upName=`echo $id | cut -d " " -f2`

    sed -ie 's/sp_$upID/$upName/g' File1
done

Problem: The sed command does not work in the loop. No change is observed in File1, at all. If I echo the sed command from the script and then run it in the terminal it works as expected. I cannot figure out what could be the problem.

Thank you for your valuable comments and solution.

Answer 1

generate a sed script from your index file (File2) instead of a loop then run that script against your File1.. It will be MUCH faster :).

 awk '{ print "s/sp_"$1"/"$2"/g"}' File2.txt > tranform.sed

then do:

 sed -i -f transform.sed File1.txt 

so your entire script could be:

awk '{ print "s/sp_"$1"/"$2"/g"}' File2.txt > transform.sed
sed -f transform.sed File1.txt

## if you want to remove your transformation file
rm transform.sed