This is a follow up to this question recapitulated below. I have the following three strings (ignoring the lines starting with >)

>chain A
---------MGPRLSVWLLLLPAALLLHEEHSRAAA--KGGCAGSGC-GKCDCHGVKGQKGERGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQA-------QVQEKG
>chain B
---------MGPRLSVWLLLLPAALLLHEEHSRAAA--KGGCAGSGC-GKCDCHGVKGQKGERGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQA-------QVQEKG
>chain C
MGRDQRAVAGPALRRWLLLGTVTVGFLAQSVLAGVKKFDVPCGGRDCSGGCQCYPEKGGRGQPGPVGPQGYNGPPGLQGFPGLQGRKGDKGERGAPGVTGPKGDVGARGVSGFPGADGIPGHPGQGGPRGRPGYDGCNGTQGDSGPQGPPGSEGFTGPPGPQGPKGQKGEP-YALPKEERDRYRGEPGEPGLVGFQGPPGRPGHVGQMGPVGAPGRPGPPGPPGPKGQQGNRGLGFYGVKGEKGDVGQPGPNGIPSDTLHPIIAPTGVTFH

I want to find out the character position of all R and D/E in the three chains that satisfy the following relationship

Ri (chain A) - Di 2 (chain B)
Ri (chain B) - Di 2 (chain C)
Ri (chain C) - Di 5 (chain A)

Explanation: Iterate over every ith R in chain A and check if the i 2 position of chain B contains D or E. If yes, output the character positions of every such R and D/E pair. Do the same with chains B C and chains C A.

Catch: While deciding the relationship, it should count the dashes. But when printing the positions it should disregard the dashes.

Using the script posted in the original question, I get the following output

B-C 187 R E

What the output should be

B-C 175-188 R E

I modified the code posted in the original question to include a correction

awk '
    { chain_id[  c]=$2                                     # save chain id, eg, "A", "B", "C"
      getline                                              # read next line from input file
      chains[c]=$0                                         # save associated chain
    }

END { i_char="R"                                           # character to search for in 1st chain

      for (i=1;i<=c;i  ) {                                 # loop through list of chains
          j= (i==c ? 1 : i 1)                              # determine index of 2nd chain
          offset= (i==c ? 5 : 2)                           #  2 for A-B, B-C;  5 for C-A

          chain_i=chains[i]                                # copy chains as we are going to cut them up as we process them
          chain_j=chains[j]
         
          
          
          chain_pair= chain_id[i] "-" chain_id[j]          # build output label, eg, "A-B"
          pos=0                                            # reset position

          while (length(chain_i)>0) {

                n=index(chain_i,i_char)                    # look for "K"
                
                if (n==0) break                            # if not found we are done with this chain pair so break out of loop else ...
                pos=pos n                                  # update our position in the chain and ...pos is the field position
                j_char=substr(chain_j,n offset,1)          # find character from 2nd chain at location n 2
                
                
                if (j_char ~ /D|E/) {
                corr_i=substr(chain_i,1,n)
                corr=gsub (/-/,"",corr_i)                  # if 2nd chain character is one of "D" or "E" then ..
                corr_pos=pos-corr
                 print chain_pair,corr_pos,i_char,j_char   # print our finding
                }

                chain_i=substr(chain_i,n 1)                # strip off 1st n characters
                chain_j=substr(chain_j,n 1)
          }
      }
    }
' file

but this doesn't help and the output is incorrect.

B-C 187 R E

CodePudding user response：

Adding some logic to keep count of dashes:

awk '
    { chain_id[  c]=$2; getline; chains[c]=$0 }
END { i_char="R"
      for (i=1;i<=c;i  ) {

          j= (i==c ? 1 : i 1)
          offset= (i==c ? 5 : 2)

          chain_i=chains[i]
          chain_j=chains[j]

          chain_pair= chain_id[i] "-" chain_id[j]
          pos=dash_cnt_i=dash_cnt_j=0

          while (length(chain_i)>0) {

                n=index(chain_i,i_char)
                if (n==0) break

                pos=pos n

                head_i = substr(chain_i,1,n)                    # copy everything up to matching character
                head_j = substr(chain_j,1,n)                    # copy everything up to matching character

                dash_cnt_i  = gsub(/-/,"",head_i)               # add count of dashes in head_i; gsub() returns number of substitutions which in this case is also the number of dashes in head_i
                dash_cnt_j  = gsub(/-/,"",head_j)               # add count of dashes in head_j

                j_char=substr(chain_j,n offset,1)

                if (j_char ~ /E|D/)
                   print chain_pair,(pos-dash_cnt_i) "-" (pos offset-dash_cnt_j) ,i_char,j_char

                chain_i=substr(chain_i,n 1)
                chain_j=substr(chain_j,n 1)
          }
      }
    }
' file.txt

This generates:

A-B 355-357 R E
A-B 390-392 R E
A-B 597-599 R D
A-B 781-783 R E
A-B 917-919 R D
A-B 968-970 R D
A-B 1063-1065 R E
A-B 1516-1518 R D
A-B 1638-1640 R E
B-C 175-188 R E                 # OP's expected result
B-C 346-364 R D
B-C 355-373 R E
B-C 396-414 R D
B-C 500-519 R D
B-C 585-602 R D
B-C 917-963 R E
B-C 1063-1108 R E
B-C 1173-1218 R D
B-C 1516-1562 R D
C-A 334-321 R E
C-A 400-389 R E
C-A 471-459 R E
C-A 740-706 R D
C-A 1228-1190 R E
C-A 1589-1552 R E