Shell Programming and Scripting

aname	val
NAME;r'(1,)	3.28584
r'(2,)<tab>
NAME;r'(3,)	6.13003
NAME;r'(4,)	4.18037
r'(5,)<tab>

r'(2,)	
r'(5,)

aname	val
NAME;r'(1,)	3.28584
NAME;r'(2,)	failed
NAME;r'(3,)	6.13003
NAME;r'(4,)	4.18037
NAME;r'(5,)	failed

# loop through incomplete file list
while read line; do 

   # remove tab from end of line
   clean_line=$(echo  $line | sed "s/\t//1")

   # create new line
   new_line='NAME;'$clean_line'\t''failed'

   # find original line and replace with modified version
   sed "s/$line/$new_line/1" final_temp1 > final_temp2

   # overwrite original file with modified file to propagate changes forward
   mv final_temp2  final_temp1

done < incomplete_case_list

sed: -e expression #1, char 160: Invalid range end
sed: -e expression #1, char 168: Invalid range end
sed: -e expression #1, char 134: Invalid range end

awk -v var1="$line" -v var2="$new_line" '{gsub(var1, var2, $0); print}' final_temp1 > final_temp2

awk: cmd. line:1: (FILENAME=final_temp1 FNR=1) fatal: Invalid range end: /1-[10-(4-amino-2-methylquinolyl)decyl]-2-methyl-4-quinolylamine_4Np.mol/

awk 'NF<2{$0="NAME;"$0"\tfailed"}1' incomplete_case_list
aname   val
NAME;r'(1,)     3.28584
NAME;r'(2,)     failed
NAME;r'(3,)     6.13003
NAME;r'(4,)     4.18037
NAME;r'(5,)     failed

#!/bin/sh

# file with list of name with incomplete output
incomplete_case_list=$1
# file being processed (replace incomplete rows with modified data)
final_temp1=$2
# output file
final_temp2=$3

# read in fail file and create array of names
while read line; do 

   # read tab separated line into array
   unset FIELD;   IFS=$'\t' read -a FIELD <<< "$line"

   # add each name to array
   fail_list=("${fail_list[@]}" "${FIELD[0]}")

done < $incomplete_case_list

# flag to avoid second print if line was replaced
replaced='0'

# loop through all rows of file to check for fail names
# check the name for each row against all names in name array, look for match
while read line; do 

   # read tab separated line into array
   unset FIELD;   IFS=$'\t' read -a FIELD <<< "$line"

   # check current line against each element in array of fail names
   for fail_name in "${fail_list[@]}"
   do

      # check name filed (0), if a match is found, print modified line
      if [ "${FIELD[0]}" == "$fail_name" ]; then

         # output modified row to next temp file
         echo -e 'NAME;'${FIELD[0]}'\t''failed' >> $final_temp2

         # set flag to indicate row has been replaced, don't print again
         replaced='1'
      fi
   done

   # if name was not found in the  fail array, print original line
   if [ "$replaced" == '0' ]; then
      echo -e ${FIELD[0]}'\t'${FIELD[1]} >> $final_temp2
   fi
   # reinitialize flag
   replaced='0'

done < $final_temp1

echo -e $line >> final_temp2