find characters present in two different lines if they satisfy a positional relationship - bash

Question

I have a peculiar problem. A text file contains the following three lines,
>chain A
---------MGPRLSVWLLLLPAALLLHEEHSRAAA--KGGCAGSGC-GKCDCHGVKGQKGERGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQA-------QVQEKGDFATKGEKGQKGEPGFQGMPGVGEKGEPGKPGPRGKPGKDGDKGEKGSPGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPGTPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPGTS-LP-GPSGRDGLPGPPGSPGPPGQPGYTNGIVECQPGPPGDQGPPGIPGQPGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGFPGQPGAKGDRGLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPGQPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDTGPPGPPGY---GPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVP--------------------LPGPPGAEGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGI-GFPGPPGPKGVDGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEP---GVGLPGLKGLPGLPGIPGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGPPGLPGSVGSPGVPGI-GPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLD-MPGPKGDKGAQGLPGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPGLPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQKGDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQAGQPGQP-GPKGDPGISGTPGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKGQAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKGSPGSVGYPGSPGLPGEKGDKGLPGLDGIPGVKGEAGLPGTPGPTGPAGQKGEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGEVGFP-GLAGSPGIPGSKGEQGFMGPPGPQGQPGLPGSPGHA-TEGPKGDRGPQGQPGLPGLPGPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGITGSKGDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGPPGPPGPYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGFDGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHG-RGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT
>chain B
---------MGPRLSVWLLLLPAALLLHEEHSRAAA--KGGCAGSGC-GKCDCHGVKGQKGERGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQA-------QVQEKGDFATKGEKGQKGEPGFQGMPGVGEKGEPGKPGPRGKPGKDGDKGEKGSPGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPGTPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPGTS-LP-GPSGRDGLPGPPGSPGPPGQPGYTNGIVECQPGPPGDQGPPGIPGQPGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGFPGQPGAKGDRGLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPGQPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDTGPPGPPGY---GPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVP--------------------LPGPPGAEGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGI-GFPGPPGPKGVDGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEP---GVGLPGLKGLPGLPGIPGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGPPGLPGSVGSPGVPGI-GPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLD-MPGPKGDKGAQGLPGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPGLPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQKGDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQAGQPGQP-GPKGDPGISGTPGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKGQAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKGSPGSVGYPGSPGLPGEKGDKGLPGLDGIPGVKGEAGLPGTPGPTGPAGQKGEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGEVGFP-GLAGSPGIPGSKGEQGFMGPPGPQGQPGLPGSPGHA-TEGPKGDRGPQGQPGLPGLPGPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGITGSKGDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGPPGPPGPYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGFDGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHG-RGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT
>chain C
MGRDQRAVAGPALRRWLLLGTVTVGFLAQSVLAGVKKFDVPCGGRDCSGGCQCYPEKGGRGQPGPVGPQGYNGPPGLQGFPGLQGRKGDKGERGAPGVTGPKGDVGARGVSGFPGADGIPGHPGQGGPRGRPGYDGCNGTQGDSGPQGPPGSEGFTGPPGPQGPKGQKGEP-YALPKEERDRYRGEPGEPGLVGFQGPPGRPGHVGQMGPVGAPGRPGPPGPPGPKGQQGNRGLGFYGVKGEKGDVGQPGPNGIPSDTLHPIIAPTGVTFHPDQYKGEKGSEGEPGIRGISLKGEEGIMGFPGLRGYPGLSGEKGSPGQKGSRGLDGYQGPDGPRGPKGEAGDPGPPGLP--AYSPHPSLAKGARGDPGFPGAQGEPGSQGEPGDPGLPGPPGLSIGDGDQRRGLPGEMGPKGFIGDPGIPALYGGPPGPDGKRGPPGPPGLPGPPGPDGFL-FGLKGAKGRAGFPGLPGSPGARGPKGWKGDAGECRCTEGDEAIKGLPGLPGPKGFAGINGEPGRKGDRGDPGQHGLPGFPGLKGVPGNIGAPGPKGAKGDS-RTITTKGERGQPGVPGVPGMKGDDGSPGRDGLDGFPGLPGPPGD-GIKGPPGDPGYPGIPGTKGTPGEMGPPGLGLPGLKGQRGFPGDAGLPGPPGFLGPPGPAGTPGQIDCDTDVKRAVGGDRQEAIQPGCIGGPKGLPGLPGPPGPTGAKGLRGIPGFAGADGGPGPRGLPGDAGREGFPGPPGFIGPRGSKGAVGLPGPDGSPGPIGLPGPDGPPGERGLPGEVLGAQPGPRGDAGVPGQPGLKGLPGDRGPPGFRGSQGMPGMPGLKGQPGLPGPSGQPGLYGPPGLHGFPGAPGQEGPLGLPGIPGREGLPGDRGDPGDTGAPGPVGMKGLSGDRGDAGFTGEQGHPGSPGFKGIDGMPGTPGLKGDRGSPGMDGFQGMPGLKGRPGFPGSKGEAGFFGIPGLKGLAGEPGFKGSRGDPGPPGPP-PVILPGMKDIKGEKGDEGPMGLKGYLGAKGIQGMPGIPGLSGIPGLPGRPGHIKGVKGDIGVPGIPGLPGFPGVAGPPGITGFPGFIGSRGDKGAPGRAGLYGEIGATGDFGDIGDT-INLPGRPGLKGERGTTGIPGLKGFFGEKGTEGDIGFPGITGVTGVQGPPGLKGQTGFPGLTGPPGSQGELGRIGLPGGKGDDGWPGAPGLPGFPGLRGIRGLHGLPGTKGFPGSPGSDIHGDPGFPGPPGERGDPGEANTLPGPVGVPGQKGDQGAPGERGPPGSPGLQGFPGITPPSNISGAPGDKGAPGIFGLKGYRGPPGPPGSAALPGSKGDTGNPGAPGTPGTKGWAGDSGPQGRPGVFGLPGEKGPRGEQGFMGNTGPTGAVGDRGPKGPKGDPGFPGAPGTVGAPGIAGIPQKIAVQPGTVGPQGRRGPPGAPGEMGPQGPPGEPGFRGAPGKAGPQGRGGVSAVPGFRGDEGPIGHQGPIGQEGAPGRPGSPGLPGMPGR-SVSIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASRNDKSYWLSTTAPLP--MMPVAEDEIKPYISRCSVCEAPAIAIAVHSQDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGGRGTCHYYANKYSFWLTTIPEQSFQGSPSADTLKAGLIRTHISRCQVCMKNL
Now, 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.
I tried to the following:
IFS=$'\n' read -d '' -r -a lines <file.txt
echo "${lines[1]}" | awk '{for(i=1;i<=length($0);i++) {if (substr($0,i,1)=="R") {print i}}}'
echo "${lines[3]}" | awk '{for(i=1;i<=length($0);i++) {if (substr($0,i,1)=="R") {print i}}}'
echo "${lines[5]}" | awk '{for(i=1;i<=length($0);i++) {if (substr($0,i,1)=="R") {print i}}}'
but this will give positions of R or E in the lines but not constrained by the relationship.

Answer 1

this can be optimized but I think works... Prints the chains compared, the position of the first match and the matched chars. Assumes chains are the same length and doesn't check for bounds. Iterates each sequence once and compares with the other two for offset match.
Note that A and B sequences are the same, so for C-A and C-B comparisons you'll get the same results.
$ awk 'function charAt(_d, _i) {return substr(_d,_i,1)}
NR%2 {chain[int(NR/2)+1]=$2; next}
{d[NR/2]=$0}
END {nc=NR/2;
for(i=1;i<=nc;i++)
for(j=1;j<=length(d[i]);j++) {
os=j+(chain[i]=="C"?5:2);
if( (c1=charAt(d[i],j))=="R") {
if( (c2=charAt(d[k=i%nc+1],os))=="D" || c2=="E") print chain[i]"-"chain[k],j,c1,c2;
if( (c2=charAt(d[k=(i+1)%nc+1],os))=="D" || c2=="E") print chain[i]"-"chain[k],j,c1,c2;
}}}' file
A-C 187 R E
A-C 365 R D
A-B 374 R E
A-C 374 R E
A-B 409 R E
A-C 415 R D
A-C 521 R D
A-C 606 R D
A-B 618 R D
A-B 829 R E
A-B 967 R D
A-C 967 R E
A-B 1018 R D
A-B 1114 R E
A-C 1114 R E
A-C 1224 R D
A-B 1569 R D
A-C 1569 R D
A-B 1692 R E
B-C 187 R E
B-C 365 R D
B-C 374 R E
B-A 374 R E
B-A 409 R E
B-C 415 R D
B-C 521 R D
B-C 606 R D
B-A 618 R D
B-A 829 R E
B-C 967 R E
B-A 967 R D
B-A 1018 R D
B-C 1114 R E
B-A 1114 R E
B-C 1224 R D
B-C 1569 R D
B-A 1569 R D
B-A 1692 R E
C-A 335 R E
C-B 335 R E
C-A 403 R E
C-B 403 R E
C-A 475 R E
C-B 475 R E
C-A 746 R D
C-B 746 R D
C-A 1236 R E
C-B 1236 R E
C-A 1600 R E
C-B 1600 R E

Answer 2

NOTE: OP hasn't provided the expected output so I'll duplicate karakfa's output format.
One awk idea:
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 "R"
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 ...
j_char=substr(chain_j,n+offset,1) # find character from 2nd chain at location n+2
if (j_char ~ /D|E/) { # if 2nd chain character is one of "D" or "E" then ...
print chain_pair,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.txt
This generates:
A-B 374 R E
A-B 409 R E
A-B 618 R D
A-B 829 R E
A-B 967 R D
A-B 1018 R D
A-B 1114 R E
A-B 1569 R D
A-B 1692 R E
B-C 187 R E
B-C 365 R D
B-C 374 R E
B-C 415 R D
B-C 521 R D
B-C 606 R D
B-C 967 R E
B-C 1114 R E
B-C 1224 R D
B-C 1569 R D
C-A 335 R E
C-A 403 R E
C-A 475 R E
C-A 746 R D
C-A 1236 R E
C-A 1600 R E