Perl versus other "scripting" languages when doing string operations

Question

I've been told that perl is a "scripting" language like the other languages mentioned in this forum.
If that's true, can these other languages handle the following spec as well as perl can?  (See spec at end of this post.)
Or is perl stronger in string operations than the other scripting languages mentioned here?
Here's the spec:
1. I give your program  a twenty-letter alphabet (any twenty letter alphabet)
For example:
ABCDEFGHIJKLMNOPQRST
2.  I also give your program four groups (any four groups) of letters in this alphabet:
For example:
s:  A,B,C,D,E
p:  F,G,H,I,J
d:  K,L,M,N,O
e:  P,Q,R,S,T
3.  I also give your program a sequence over the twenty-letter alphabet that I gave you in Step (1) above:
For example:
ABCDEFGHIJKLMNOPQRSTSRQPONMLKJIHGFEDCBA
4.  Given this sequence,you search for pairs of adjacent letters (x,y) where X and y are from different groups (the groups defined in Step (2) above.)
Also, you return the results of this search by giving me back the following two strings:
ABCD(EF)GHI(JK)LMN(OP)QRSTSRQ(PO)NML(KJ)IHG(FE)DCBA  
ABCD(sp)GHI(pd)LMN(de)QRSTSRQ(ed)NML(dp)IHG(ps)DCBA
5.  Note: if I give you a sequence that contains "overlapping" ordered pairs like:
...EFK...
then you ignore the second ordered pair.  That is, you return:
...(EF)K

Answer 1

OK - here is the final stuff on the "C" side.
To execute the program, the command line is:
20let.exe file1.txt file2.txt file3.txt > fileout.txt
Below, I've provided:
a) source code 20let.c
b) sample input file1.txt
c) sample input file2.txt
d) sample input file3.txt
e) output fileout.txt generated from these input files.
As soon as Bill finishes the perl version of the source code, I'll post that also.
source code of 20let.c
// 20let.c5
#include <stdio.h>
#include <stdlib.h>
int T[333],A[99999],G[333],B[99999],C[99999],N[299999],P[99999];
int n1,n2,f,p,x1,x2,n,m,a,b,c,i,j,k,x,y,z;
int E[233][233];
FILE *file;
int substrings(int x1,int x2);
int main(int argc, char*argv[]) {
    if(argc<3){
        printf("\nusage:20let protein-file nucleotide-file pairs-include-file\n\n");
        printf("marks amino-acid-pairs from different groups in protein-file\n");
        printf("iff they are in the include-file\n");
        exit(1);
//----------------define the groups        G['I'] = 's', e.g.
    x='s'; G['I']=x;G['M']=x;G['V']=x;G['A']=x;G['G']=x;
    x='p'; G['F']=x;G['L']=x;G['P']=x;G['W']=x;G['W']=x;
    x='d'; G['H']=x;G['Q']=x;G['D']=x;G['E']=x;G['E']=x;
    x='t'; G['S']=x;G['T']=x;G['Y']=x;G['N']=x;G['C']=x;G['K']=x;G['R']=x;
//----------------the 4 bases              T['a'] = 0 thru 3
    for(x=0;x<222;x++)
        T[x]=-999;
    T['a']=0;T['c']=1;T['g']=2;T['t']=3;
    T['A']=0;T['C']=1;T['G']=2;T['T']=3;
  for(i=65;i<70;i++)G<i>='s';
  for(i=70;i<75;i++)G<i>='p';
  for(i=75;i<80;i++)G<i>='d';
  for(i=80;i<85;i++)G<i>='t';
//---------------- read include-file   file3 xxxyyy pairs E[x][y] of interest
    f=0;
    for(x=0;x<222;x++)
        for(y=0;y<222;y++)
            E[x][y]=0;
    if((file=fopen(argv[3],"rb"))==NULL){
        printf("\ncan't open exclude-file %s\n",argv[1]);exit(1);
mq1: if(feof(file))
        goto mq3;
    x=fgetc(file);y=fgetc(file);x=fgetc(file);
    x=T[fgetc(file)]*16+T[fgetc(file)]*4+T[fgetc(file)];
    y=T[fgetc(file)]*16+T[fgetc(file)]*4+T[fgetc(file)];
    if(x<64 && x>=0 && y<64 && y>=0){
        E[x][y]=1;
        f++;
mq2: if(feof(file))
        goto mq3;
    a=fgetc(file);
    if(a!=10)
        goto mq2;
    goto mq1;
mq3: fclose(file);
//------------------read amino-acid file    file1 == P array
    if((file=fopen(argv[1],"rb"))==NULL){
        printf("\ncan't open file %s\n",argv[1]);exit(1);}
    p=0;
m1p: if(feof(file))
        goto m2p;
    p++;
    P[p]=fgetc(file);
    if(G[P[p]]==0)
        p--;
    goto m1p;
m2p:;
    fclose(file);
//------------------read nucleotide file    file2 == N array
    if((file=fopen(argv[2],"rb"))==NULL){
        printf("\ncan't open file %s\n",argv[1]);exit(1);
    n=0;
m1n: if(feof(file))
        goto m2n;
    n++;
    N[n]=fgetc(file);
    if(N[n]!='a' && N[n]!='c' && N[n]!='g' && N[n]!='t')
        n--;
    goto m1n;
m2n:;
    fclose(file);
//for(i=1;i<=p;i++)printf("%c",P<i>);printf("\n");
//for(i=1;i<=n;i++)printf("%c",N<i>);printf("\n");
//printf("%i include-pairs  %i nucleotides  %i proteins\n",f,n,p);
//------------1st line------------------       B<i> = result
    m=0;
    for(i=1;i<=p;i++){
        n1=T[N[i*3-2]]*16+T[N[i*3-1]]*4+T[N[i*3]];
        n2=T[N[i*3+1]]*16+T[N[i*3+2]]*4+T[N[i*3+3]];
//printf("\ni=%i p=%i n1=%i n2=%i\n",i,p,n1,n2);
        if(E[n1][n2]<1 || G[P<i>]==G[P[i+1]] /* || i==n */){
            printf("%c",P<i>);
            m++;
            B[m]=P<i>;
            goto m3;
        printf("(%c%c)",P<i>,P[i+1]);
        i++;
        m++;
        B[m]='(';
        m++;
        B[m]=P[i-1];
        m++;
        B[m]=P<i>;
        m++;
        B[m]=')';
//printf("(%c)%c",G[A<i>],G[A[i+1]]);i++;
    m3:;
    printf("\n");
//------------2nd line------------------       C<i> = result
    m=0;
    for(i=1;i<=p;i++){
        n1=T[N[i*3-2]]*16+T[N[i*3-1]]*4+T[N[i*3]];
        n2=T[N[i*3+1]]*16+T[N[i*3+2]]*4+T[N[i*3+3]];
        if(E[n1][n2]<1 || G[P<i>]==G[P[i+1]] /* || i==n */){
            printf("%c",P<i>);
            m++;
            C[m]=P<i>;
            goto m4;
        printf("(%c%c)",G[P<i>],G[P[i+1]]);
        i++;
        m++;
        C[m]='(';
        m++;
        C[m]=G[P[i-1]];
        m++;
        C[m]=G[P<i>];
        m++;
        C[m]=')';
//printf("(%c)%c",G[A<i>],G[A[i+1]]);i++;
    m4:;
    printf("\n");
//for(i=1;i<=m;i++)printf("%c",B<i>);printf("\n");
//------------3rd line------------------         printf only
    m=0;
    for(i=1;i<=p;i++){
        n1=T[N[i*3-2]]*16+T[N[i*3-1]]*4+T[N[i*3]];
        n2=T[N[i*3+1]]*16+T[N[i*3+2]]*4+T[N[i*3+3]];
        if(E[n1][n2]<1 || G[P<i>]==G[P[i+1]] /* || i==n */){
            printf("%c%c%c",N[i*3-2],N[i*3-1],N[i*3]);
            goto m33;
        printf("(%c%c%c%c%c%c)",N[i*3-2],N[i*3-1],N[i*3],N[i*3+1],N[i*3+2],N[i*3+3]);
        i++;
    m33:;
    printf("\n");
//--------------substrings------------
    substrings(20,29);
    substrings(30,39);
    substrings(40,49);
    substrings(50,59);
    substrings(60,69);
    return 0;
int substrings(int x1,int x2)
    printf("\n");
    printf("lengths %i - %i : \n",x1,x2);
    for(i=1; i<p; i++)
        for (j=i+x1; j<i+x2; j++) {
            if (C<i>>95 && C[j]>95) {   // if lc letter in line2
                for(x=i;x<=j;x++)
                    printf("%c",C[x]);
                printf("|");
                for(x=i;x<=j;x++)
                    if(B[x]>44)         // if not () in line 1
                        printf("%c",B[x]);
                printf("|");
                for(x=i;x<=j;x++)
                    if(C[x]>95)         // if lc letter line2
                        printf("%c",C[x]);
                printf("\n");}
input file1.txt
MKKHTDQPIADVQGSPDTRH
IAIDRVGIKAIRHPVLVADK
DGGSQHTVAQFNMYVNLPHN
FKGTHMSRFVEILNSHEREI
SVESFEEILRSMVSRLESDS
GHIEMTFPYFVNKSAPISGV
KSLLDYEVTFIGEIKHGDQY
GFTMKVIVPVTSLCPCSKKI
SDYGAHNQRSHVTISVHTNS
FVWIEDVIRIAEEQASCELF
GLLKRPDEKYVTEKAYNNPK
FVEDIVRDVAEILNHDDRID
AYVVESEBFESIHNHSAYAL
IERD
input file2.txt
atgaaaaaacatactgatcaacctatcgctgatgtgcagggctcaccggataccagacat
atcgcaattgacagagtcggaatcaaagcgattcgtcacccggttctggtcgccgataag
gatggtggttcccagcataccgtggcgcaatttaatatgtacgtcaatctgccacataat
ttcaaagggacgcatatgtcccgttttgtggagatactaaatagccacgaacgtgaaatt
tcggttgaatcatttgaagaaattttgcgctccatggtcagcaggctggaatcagattcc
ggccatattgaaatgacttttccctacttcgtcaataaatcagcccctatctcaggtgta
aaaagcttgctggattatgaggtaacctttatcggcgaaattaaacatggcgatcaatat
gggtttaccatgaaggtgatcgttcctgttaccagcctgtgcccctgctccaagaaaata
tccgattacggtgcgcataaccagcgttcacacgtcaccatttctgtacacactaacagc
ttcgtctggattgaggacgttatcagaattgcggaagaacaggcctcatgcgaactgttc
ggtctgctgaaacggccggatgaaaaatatgtcacagaaaaggcctataacaatccgaaa
tttgtcgaagatatcgtccgtgatgtcgccgaaatacttaatcatgatgaccggatagat
gcctatgttgttgaatcagaaaactttgaatccatacataatcactctgcatacgcactg
atagagcgcgac
input file3.txt
FA tttgcc
FA ttcgcc
FA tttgct
FA ttcgct
LK ttaaaa
LK ttgaaa
LK ttaaag
LK ttgaag
LS ctgctc
LS ctgctt
LS ctactc
LS ctactt
LT ctcacc
LT ctcact
LT cttacc
LT cttact
LY ctctac
LY ctctat
LY ctttac
LY ctttat
LG ctcggc
LG ctcggt
LG cttggc
LG cttggt
IP attccc
IP attcct
IP atcccc
IP atccct
IP attcca
IP attccg
IP atccca
IP atcccg
ML atgctc
ML atgctt
ML atgctc
ML atgctt
VL gtgctg
VL gtgcta
VL gtactg
VL gtacta
VS gtgtcc
VS gtatct
VS gtgtcc
VS gtatct
VT gtcacc
VT gtcact
VT gttacc
VT gttact
VS gtcagc
VS gtcagt
VS gttagc
VS gttagt
SL tcgctg
SL tcgcta
SL tcactg
SL tcacta
SP tctcca
SP tctccg
SP tcccca
SP tccccg
PV ccggtg
PV ccggta
PV ccagtg
PV ccagta
PG cccggc
PG cccggt
PG cctggc
PG cctggt
TL acgctg
TL acgcta
TL acactg
TL acacta
TP acgccg
TP acgcca
TP acaccg
TP acacca
AL gcttta
AL gctttg
AL gcctta
AL gccttg
AP gcgccg
AP gcgcca
AP gcaccg
AP gcacca
AP gctcca
AP gctccg
AP gcccca
AP gccccg
AN gctaat
AN gctaac
AN gccaat
AN gccaac
AS gccagc
AS gccagt
AS gctagc
AS gctagt
YP tatccg
YP tatcca
YP tacccg
YP taccca
HP catccg
HP catcca
HP cacccg
HP caccca
QR cagcga
QR cagcgg
QR caacga
QR caacgg
DL gatttg
DL gattta
DL gacttg
DL gactta
EN gaaaat
EN gaaaac
EN gagaat
EN gagaac
EK gaaaaa
EK gaaaag
EK gagaaa
EK gagaag
ER gagcga
ER gagcgg
ER gaacga
ER gaacgg
WR tggcga
WR tggcgg
RV cgggtg
RV cgggta
RV cgagtg
RV cgagta
RW cggtgg
RW cgatgg
SG agtgga
SG agtggg
SG agcgga
SG agcggg
GF ggtttt
GF ggtttc
GF ggcttt
GF ggcttc
GL gggctg
GL gggcta
GL ggactg
GL ggacta
GY gggtat
GY gggtac
GY ggatat
GY ggatac
GY ggttat
GY ggttac
GY ggctat
GY ggctac
GK ggaaaa
GK ggaaag
GK gggaaa
GK gggaag
GK ggcaag
GK ggcaaa
GK ggtaag
GK ggtaaa
GW ggctgg
GW ggttgg
GR gggcgg
GR gggcga
GR ggacgg
GR ggacga
GS ggcagc
GS ggcagt
GS ggtagc
GS ggtagt
output fileout.txt
MKKHTDQPIADVQGSPDTRHIAIDRVGIKAIR(HP)VLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSM(VS)RLESDSGHIEMTFPYFVNKSAPISGVKSLLDYEVTFIGEIKHGDQYGFTMKVIVP(VT)SLCPCSKKISDYGAHNQRSH(VT)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(EK)YVT(EK)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(EF)ESIHNHSAYALIERD
MKKHTDQPIADVQGSPDTRHIAIDRVGIKAIR(dp)VLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSM(st)RLESDSGHIEMTFPYFVNKSAPISGVKSLLDYEVTFIGEIKHGDQYGFTMKVIVP(st)SLCPCSKKISDYGAHNQRSH(st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt)YVT(dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(dp)ESIHNHSAYALIERD
atgaaaaaacatactgatcaacctatcgctgatgtgcagggctcaccggataccagacatatcgcaattgacagagtcggaatcaaagcgattcgt(cacccg)gttctggtcgccgataaggatggtggttcccagcataccgtggcgcaatttaatatgtacgtcaatctgccacataatttcaaagggacgcatatgtcccgttttgtggagatactaaatagccacgaacgtgaaatttcggttgaatcatttgaagaaattttgcgctccatg(gtcagc)aggctggaatcagattccggccatattgaaatgacttttccctacttcgtcaataaatcagcccctatctcaggtgtaaaaagcttgctggattatgaggtaacctttatcggcgaaattaaacatggcgatcaatatgggtttaccatgaaggtgatcgttcct(gttacc)agcctgtgcccctgctccaagaaaatatccgattacggtgcgcataaccagcgttcacac(gtcacc)atttctgtacacactaacagcttcgtctggattgaggacgttatcagaattgcggaagaacaggcctcatgcgaactgttcggtctgctgaaacggccggat(gaaaaa)tatgtcaca(gaaaag)gcctataacaatccgaaatttgtcgaagatatcgtccgtgatgtcgccgaaatacttaatcatgatgaccggatagatgcctatgttgttgaatca(gaaaac)tttgaatccatacataatcactctgcatacgcactgatagagcgc
lengths 20 - 29 :
st)SLCPCSKKISDYGAHNQRSH(s|VTSLCPCSKKISDYGAHNQRSHV|sts
st)SLCPCSKKISDYGAHNQRSH(st|VTSLCPCSKKISDYGAHNQRSHVT|stst
t)SLCPCSKKISDYGAHNQRSH(s|TSLCPCSKKISDYGAHNQRSHV|ts
t)SLCPCSKKISDYGAHNQRSH(st|TSLCPCSKKISDYGAHNQRSHVT|tst
lengths 30 - 39 :
st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(d|VTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDE|std
t)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(d|TISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDE|td
t)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt|TISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEK|tdt
dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(d|EKAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESE|dtd
dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(dp|EKAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESEF|dtdp
t)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(d|KAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESE|td
t)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(dp|KAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESEF|tdp
lengths 40 - 49 :
st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt)YVT(d|VTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEKYVTE|stdtd
st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt)YVT(dt|VTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEKYVTEK|stdtdt
t)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt)YVT(d|TISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEKYVTE|tdtd
t)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt)YVT(dt|TISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEKYVTEK|tdtdt
dt)YVT(dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(d|EKYVTEKAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESE|dtdtd
dt)YVT(dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(dp|EKYVTEKAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESEF|dtdtdp
t)YVT(dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(d|KYVTEKAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESE|tdtd
t)YVT(dt)AYNNPKFVEDIVRDVAEILNHDDRIDAYVVES(dp|KYVTEKAYNNPKFVEDIVRDVAEILNHDDRIDAYVVESEF|tdtdp
lengths 50 - 59 :
t)RLESDSGHIEMTFPYFVNKSAPISGVKSLLDYEVTFIGEIKHGDQYGFTMKVIVP(s|SRLESDSGHIEMTFPYFVNKSAPISGVKSLLDYEVTFIGEIKHGDQYGFTMKVIVPV|ts
lengths 60 - 69 :
dp)VLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSM(s|HPVLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSMV|dps
dp)VLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSM(st|HPVLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSMVS|dpst
p)VLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSM(s|PVLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSMV|ps
p)VLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSM(st|PVLVADKDGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSMVS|pst
st)RLESDSGHIEMTFPYFVNKSAPISGVKSLLDYEVTFIGEIKHGDQYGFTMKVIVP(st|VSRLESDSGHIEMTFPYFVNKSAPISGVKSLLDYEVTFIGEIKHGDQYGFTMKVIVPVT|stst
st)SLCPCSKKISDYGAHNQRSH(st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(d|VTSLCPCSKKISDYGAHNQRSHVTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDE|ststd
st)SLCPCSKKISDYGAHNQRSH(st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt|VTSLCPCSKKISDYGAHNQRSHVTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEK|ststdt
t)SLCPCSKKISDYGAHNQRSH(st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(d|TSLCPCSKKISDYGAHNQRSHVTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDE|tstd
t)SLCPCSKKISDYGAHNQRSH(st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt|TSLCPCSKKISDYGAHNQRSHVTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEK|tstdt
t)SLCPCSKKISDYGAHNQRSH(st)ISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPD(dt)YVT(d|TSLCPCSKKISDYGAHNQRSHVTISVHTNSFVWIEDVIRIAEEQASCELFGLLKRPDEKYVTE|tstdtd
Edited by: David Halitsky on Mar 18, 2008 4:21 AM
Edited by: David Halitsky on Mar 18, 2008 4:22 AM