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pepx.c
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// For now update both at git github.com/calipho-sib/pepx and svn http://trac/svn/NextProt/main/trunk/com.genebio.nextprot.tools.sequence
#include <stdio.h>
#include <ctype.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
//#include <sys/syscall.h>
#include <errno.h>
#include <getopt.h>
#include <malloc.h>
#define FALSE 0
#define TRUE 1
#define MAXSEQ 32768
// MAXSEQ max number of results for a query
#define MAXHEADSIZE 1500000
// MAXHEADSIZE size of titin longest isoform header line in PEFF
#define MAXSEQSIZE 36500
// MAXSEQSIZE = size of titin longest isoform
#define MAXISO 100
#define MAXVARINPEP 127
#define MAXVARPERAA 8
#define LINELEN 1024
#define ACLEN 16
//#define BINSIZE 32 // adjust w stats
#define BINSIZE 16 // adjust w stats, this is becoming a problem, have to reduce to 12 when indexing with variants !
// optimal binsizes: 2->1000, 3->100, 4->25, 5->10, 6->?
#define MINPEPSIZE 3
#define MAXPEPSIZE 7
// Allowing 7 implies adapting BINSIZE t0 low value in 7-mers (memory pbs)
#define SILENT 1
#define INDEX2WIDTH 12
#ifndef max
#define max( a, b ) ( ((a) > (b)) ? (a) : (b) )
#endif
// Globals
typedef struct idxdata
{
FILE *fh;
FILE *ffh;
int elemcnt;
} IDXDATA;
IDXDATA idxinfo[MAXPEPSIZE], idxinfoIL[MAXPEPSIZE];
FILE *currentindex;
char currentresult[32];
static int currentpepsize; // weird but alters idxinfo[6] when changed if not static
typedef struct bin
{
int ac_cnt;
struct bin *nextbinptr;
char ac[BINSIZE][ACLEN];
} BIN;
BIN **toplevel[MAXPEPSIZE + 1];
int varindex_overflow_cnt = 0;
char variants[MAXSEQSIZE][MAXVARPERAA];
char results[MAXSEQ][ACLEN];
int aacode[26] = {0, 2, 1, 2, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, -1, 12, 13, 14, 15, 16, 1, 17, 18, -1, 19, 3};
// B is D, Z is E, U is C, J is I
char aarevcode[] = "ACDEFGHIKLMNPQRSTVWY";
char aarevcodeIL[] = "ACDEFGHJKLMNPQRSTVWY";
char matchmode[10] = "ACISO";
int pow20[] = {1, 20, 400, 8000, 160000, 3200000, 64000000, 1280000000};
int binsizes[] = {0, 0, 1000, 100, 25, 10, 6, 4};
char masterseq[MAXSEQSIZE];
char currAC[ACLEN];
char currISO[ACLEN];
char outputmode[16];
char linesep[4] = "\n";
char envstring[LINELEN];
char version[] = "1.72";
// debug/profiling/stats stuff
int debug;
int totalbins = 0;
clock_t start;
double duration;
int umatchcnt;
int maxoccur = 0;
int usscnt = 0;
int totalvarcnt = 0;
int varmisscnt1 = 0, varmisscnt2 = 0, varmisscnt3 = 0;
int ignore_variants = 0;
int IL_merge = 0;
int sevenmers_only = 0;
int json = 0;
int FASTAinput = 0;
int mINPEPSIZE = 3;
int mAXPEPSIZE = MAXPEPSIZE - 1; // default to 6-mers
static char jsonBuffer[8192];// weird but alters idxinfo[6] when changed if not static
char varfolder[LINELEN];
char indexfolder[LINELEN] = ".";
// ---------------- code4tenAA ---------------------
char *code4tenAA(char *currentAC)
{
int i, found = 0;
static char codedAC[16] = "";
static char *tab[] = {"A A0A024", "B A0A044", "C A0A067", "D A0A075", "E A0A087", "F A0A088", "G A0A096", "H A0A0A0", "I A0A0A6", "J A0A0B4", "K A0A0C3",
"L A0A0C4", "M A0A0C5", "N A0A0D2", "O A0A0D5", "P A0A0D9", "Q A0A0E3", "R A0A0G2", "S A0A0H2", "T A0A0J9", "U A0A0K0", "V A0A0M3", "W A0A0N4",
"X A0A0R4", "Y A0A0S2", "Z A0A0U1", "a A0A0U5", "b A0A0X1", "c A0A140", "d A0A182", "e A0A1B0", "f A0A1C7", "g A0A1D5", "h A0A1W2", "i A0A286",
"j A0A2R8", "k A0A0K2"
};
if(!strncmp(currentAC, "P", 1))
// convert back to 10 digit AC
{
strncpy(codedAC, currentAC + 1, 1);
codedAC[1] = 0;
for(i = 0; i < sizeof(tab) / 8; i++)
if(!strncmp(tab[i], codedAC, 1))
{
found = 1;
break;
}
if(found)
{
strcpy(codedAC, tab[i] + 2);
strcat(codedAC, currentAC + 2);
//fprintf(stderr,"output: %s\n",codedAC);
return(codedAC);
}
else
strcpy(codedAC, "XXXXXX");
}
else
// convert to 6 digit AC
{
strncpy(codedAC, currentAC, 6);
codedAC[6] = 0;
for(i = 0; i < sizeof(tab) / 8; i++)
if(strstr(tab[i], codedAC))
{
found = 1;
break;
}
if(found)
{
strcpy(codedAC, "P");
strncat(codedAC, tab[i], 1);
strcat(codedAC, currentAC + 6);
}
else
strcpy(codedAC, "XXXXXX");
}
//fprintf(stderr,"output: %s\n",codedAC);
return(codedAC);
}
// ---------------- code2sseq ---------------------
void code2sseq(int sseqcode, int pepsize, char *subseq)
{
char sseq[16] = "";
int i, j;
for(i = pepsize - 1; i >= 0; i--)
{
j = sseqcode / pow20[i];
sseqcode %= pow20[i];
if(IL_merge)
strncat(sseq, &aarevcodeIL[j], 1);
else
strncat(sseq, &aarevcode[j], 1);
}
strcpy(subseq, sseq);
}
// ---------------- sscode ---------------------
int sscode(char *subseq)
{
int sseqcode = 0, len, i;
len = strlen(subseq);
for(i = len; i > 0; i--)
sseqcode += pow20[len - i] * (aacode[subseq[i - 1] - 'A']);
return(sseqcode);
}
// ---------------- pepx_json_header---------------------
void pepx_json_header(char *title, char *querystring, int modeIL)
// recapitulates given parameters
{
sprintf(jsonBuffer, "\"%s\":{\n", title);
fputs(jsonBuffer, stdout); // outputs header title
if(querystring != NULL)
{
sprintf(jsonBuffer, "\"peplist\":\"%s\",\n\"modeIL\": %d\n},", querystring, modeIL);
fprintf(stdout, "%s", jsonBuffer);
//fprintf(stderr,"jsonBuffer: %s\n",jsonBuffer);
}
}
// ---------------- pepx_tojson ---------------------
char *pepx_tojson(char *finalresult)
{
int varpos = 0;
char *dashptr;
//fprintf(stdout,"pepx_tojson receives %s\n",finalresult);
dashptr = strrchr(finalresult, '-');
if((dashptr != finalresult + 6) && (dashptr != finalresult + 10)) // don't forget 10 digirs
// we have a variant pos in the last digits (eg: NX_Q8IWA4-2-121)
{
varpos = atoi(dashptr + 1);
*dashptr = 0; // remove parsed pos from string
}
sprintf(jsonBuffer, "{\n\"isoformName\":\"%s\",\n\"position\":%d\n}", finalresult, varpos);
return(jsonBuffer);
}
// ---------------- pepx_create_variant_files ---------------------
int pepx_create_variant_files(char *varfolder)
{
FILE *varmaster, *out;
char *token, buf[LINELEN], entryvarbuf[524288] = "", org[64], dest[128], fname[128], lastac[16] = "", ac[16], nxid[16], annotId[32];
int startpos, endpos, i = 0;
fprintf(stderr, "Building for first time with variants, please wait...\n");
sprintf(fname, "pepx-variantdata.csv");
if((varmaster = fopen(fname, "r")) == NULL)
{
perror(fname);
return(0);
}
while(fgets(buf, LINELEN, varmaster))
// Sample line: "NX_P16333-1,AN_P16333_000975,183,183,V,I", actually commas are replaced by spaces
{
if(strncmp(buf, "NX_", 3))
continue;
*dest = 0; //To avoid that last value is keeped when scaning a miss variant (dest empty)
sscanf(buf, "%s %s %d %d %s %s\n", nxid, annotId, &startpos, &endpos, org, dest);
//fprintf(stderr,"read %s\n",buf);
//fprintf(stderr,"nxid: %s\n",nxid);
strcpy(ac, nxid + 3);
if(strlen(lastac) && strcmp(ac, lastac))
// write previous iso record
{
sprintf(fname, "%s/%s.csv", varfolder, lastac);
//fprintf(stderr,"writing %s\n",fname);
out = fopen(fname, "w");
fprintf(out, "%s", entryvarbuf);
fclose(out);
if((++i % 2500) == 0)
fprintf(stderr, "%d isoform variant files created...\n", i);
sprintf(buf, "%d %d %s %s\n", startpos, endpos, org, dest);
strcpy(entryvarbuf, buf);
strcpy(lastac, ac);
}
else
{
sprintf(buf, "%d %d %s %s\n", startpos, endpos, org, dest);
strcat(entryvarbuf, buf);
strcpy(lastac, ac);
}
}
// write last record
sprintf(fname, "%s/%s.csv", varfolder, ac);
out = fopen(fname, "w");
fprintf(out, "%s", entryvarbuf);
fclose(out);
sprintf(fname, "%s/VARIANTS_OK", varfolder); // flag file
out = fopen(fname, "w");
fclose(out);
return(1);
}
// ---------------- pepx_build_varindex ---------------------
int pepx_build_varindex(char *isoname)
{
char buf[LINELEN], orgAA[16], lastorgAA[16], varAA[16], fname[64], *ptr;
char iso[16];
int i, skipvar = 0, cmdres, fpos, lastfpos, lpos, localvarcnt = 0;
FILE *NextProtvariants;
if(debug)
fprintf(stderr, "Building variants for %s\n", currISO);
if(is10digits(isoname))
// get around 10-len accs
{
strcpy(iso, code4tenAA(isoname));
}
else strcpy(iso, isoname);
// Get variants from NextProt files
sprintf(fname, "%s/%s.csv", varfolder, iso);
if(debug) fprintf(stderr, "opening file: %s\n", fname);
if((NextProtvariants = fopen(fname, "r")) == NULL)
// THe variant file doesn't exist for this iso : no variants
return(0);
// Reset table each time
memset(variants, 0, MAXSEQSIZE * MAXVARPERAA);
// Todo: check that orgAA is exactly the same (seq/vars desynchronization)
while(fgets(buf, LINELEN, NextProtvariants))
{
*varAA = 0; //To avoid that last value is keeped when scaning a miss variant (varAA empty)
if(debug) fprintf(stderr, "variants line: %s\n", buf);
sscanf(buf, "%d %d %s %s\n", &fpos, &lpos, orgAA, varAA);
//if(strstr(iso,"P04637") && strstr(buf,"description") && strstr(buf,"sporadic"))
if(fpos == 1 || strchr(varAA, '*') || (strlen(orgAA) > 2) || (strlen(varAA) > 2))
// No variants on Met-1 allowed, No stop variants allowed, No long variants
{
if((strlen(varAA) == 1 && orgAA[strlen(varAA) - 1] == varAA[0]) || strlen(varAA) == 0)
varmisscnt3++;
skipvar = 1;
}
if(skipvar)
{
skipvar = 0;
continue;
}
if((fpos != lpos)) // not a simple snp
{
if((strlen(orgAA) == 2) && (strlen(varAA) == 2) && orgAA[0] == varAA[0])// like A7XYQ1(180-181)
// Store variant at 2nd pos
{
if(IL_merge && (varAA[1] == 'I' || varAA[1] == 'L') )
varAA[1] = 'J';
variants[fpos][0] = varAA[1];
localvarcnt++;
}
else if((strlen(orgAA) == 2) && (strlen(varAA) == 1) && varAA[0] == orgAA[1]) // like A6NFR6-3
// Store variant
{
if((fpos == lastfpos + 1) && (orgAA[0] == lastorgAA[0])) // To avoid damage like in O00555-1 2219-2220 and 2220-2221
{
lastfpos = fpos;
continue;
}
variants[fpos - 1][0] = 'X'; // Missing
varmisscnt2++;
strcpy(lastorgAA, orgAA);
lastfpos = fpos;
localvarcnt++;
}
}
else
{
if(IL_merge && ((orgAA[0] == 'I' && varAA[0] == 'L') || (orgAA[0] == 'L' && varAA[0] == 'I'))) // In IL mode variants I->L or L->I would just add noise and are ignored
continue;
// Store variant
if(strlen(varAA) == 0)
// code for 'Missing' AA
{
strcpy(varAA, "X");
varmisscnt1++;
}
for(i = 0; i < MAXVARPERAA; i++)
// we allow 8 different variants at each position: Check if we already have a variant at this pos
if(variants[fpos - 1][i] == 0)
break;
//if(i >= MAXVARPERAA) fprintf(stderr,"%s: multiple variants at %d-%d\n",currISO,fpos,lpos);
if(IL_merge && (varAA[0] == 'I' || varAA[0] == 'L') )
varAA[0] = 'J';
variants[fpos - 1][i] = varAA[0];
localvarcnt++;
}
}
fclose(NextProtvariants);
if(debug)
fprintf(stderr, "Variants done.\n");
return(localvarcnt);
}
// ---------------- pepx_loadall ---------------------
void pepx_loadall()
{
int i, pepcnt, filelen;
char fname[LINELEN], *ptr, idxpath[128] = "";
FILE *idx;
if(strlen(indexfolder) > 8)
{
strcpy(idxpath, indexfolder);
strcat(idxpath, "/");
}
else if((ptr = getenv("PEPX")) != NULL)
{
strcpy(idxpath, ptr);
strcat(idxpath, "/");
}
// Check if we've indexed small-mers
sprintf(fname, "%spepxIL3.idx", idxpath);
if((idx = fopen(fname, "r")) == NULL)
{
sprintf(fname, "%spepx3.idx", idxpath);
if((idx = fopen(fname, "r")) == NULL)
// Indexed only with 7-mers
mINPEPSIZE = mAXPEPSIZE = MAXPEPSIZE;
}
for(i = mINPEPSIZE; i <= mAXPEPSIZE; i++)
{
usscnt = 0;
if(IL_merge)
sprintf(fname, "%spepxIL%d.idx", idxpath, i);
else
sprintf(fname, "%spepx%d.idx", idxpath, i);
if((idx = fopen(fname, "r")) == NULL)
{
perror(fname);
exit(2);
}
// save flat file handle
if(IL_merge)
idxinfoIL[i].ffh = idx;
else
idxinfo[i].ffh = idx;
strcat(fname, "2"); // secundary index name
if((idx = fopen(fname, "r")) == NULL)
{
perror(fname);
exit(2);
}
fseek(idx, 0, SEEK_END);
filelen = ftell(idx);
pepcnt = filelen / (i + INDEX2WIDTH);
//printf("%d-mers size: %d bytes -> %d elts\n",i,filelen,pepcnt);
if(IL_merge)
{
idxinfoIL[i].fh = idx;
idxinfoIL[i].elemcnt = pepcnt;
}
else
{
idxinfo[i].fh = idx;
idxinfo[i].elemcnt = pepcnt;
}
}
}
// ---------------- pepx_initindexes ---------------------
void pepx_initindexes()
{
int pepsize;
BIN **ptr;
for(pepsize = mINPEPSIZE; pepsize <= mAXPEPSIZE; pepsize++)
{
if((ptr = calloc(1, pow20[pepsize] * sizeof(BIN *))) == NULL)
{
fprintf(stderr, "Allocation failed\n");
exit(11);
}
//printf("%d empty ints reserved at address %p\n",pow20[pepsize],ptr);
toplevel[pepsize] = ptr;
}
}
// ---------------- pepx_save ---------------------
void pepx_save(char *fname, int pepsize)
{
int sseqcode, i, maxcode, ac_cnt, iso_cnt;
char ac[ACLEN], ac_noiso[ACLEN], lastac[ACLEN], subseq[16], maxseq[16] = "";
FILE *out, *out2;
BIN *binptr, **binarray;
int idxpos;
if((out = fopen(fname, "w")) == NULL)
{
perror(fname);
exit(2);
}
// secundary index
strcat(fname, "2");
if((out2 = fopen(fname, "w")) == NULL)
{
perror(fname);
exit(2);
}
// index header line (1rst pep line must not be at pos 0 for new index schema)
for(i = 0; i < pepsize + INDEX2WIDTH - 1; i++)
fprintf(out2, "0");
fprintf(out2, "\n");
usscnt = maxoccur = umatchcnt = 0;
fprintf(stderr, "Writing index for %d-mers ...\n", pepsize);
binarray = toplevel[pepsize];
maxcode = pow20[pepsize];
for(sseqcode = 0; sseqcode < maxcode; sseqcode++)
if((binptr = binarray[sseqcode]) != NULL)
// This pep has some matches
{
code2sseq(sseqcode, pepsize, subseq);
idxpos = ftell(out);
if(fprintf(out, "%s\n", subseq) <= 0)
fprintf(stderr, "writing acs for %s failed\n", subseq);
// write secundary index
fprintf(out2, "%s %10u\n", subseq, idxpos);
ac_cnt = iso_cnt = 0;
usscnt++;
while(binptr->nextbinptr != NULL)
{
// add the next BINSIZE ac
for(i = 0; i < BINSIZE; i++)
{
strcpy(ac, binptr->ac[i]);
fprintf(out, "%s\n", ac);
//fprintf(stderr,"ac: %s\n",ac);
iso_cnt++;
strcpy(ac_noiso, ac);
ac_noiso[6] = 0;
if(ac_noiso != lastac)
ac_cnt++;
strcpy(lastac, ac_noiso);
}
// set pointer to next bin
binptr = binptr->nextbinptr;
}
// dump last bin
for(i = 0; i < binptr->ac_cnt; i++)
{
strcpy(ac, binptr->ac[i]);
fprintf(out, "%s\n", ac);
iso_cnt++;
strcpy(ac_noiso, ac);
ac_noiso[6] = 0;
if(ac_noiso != lastac)
ac_cnt++;
strcpy(lastac, ac_noiso);
}
if(ac_cnt == 1)
umatchcnt++;
else if(ac_cnt > maxoccur)
{
maxoccur = ac_cnt;
strcpy(maxseq, subseq);
}
}
fprintf(stderr, "%d distincts %d-mer, %d are uniques (found in just 1 entry), most frequent: %s (%d)\n", usscnt, pepsize, umatchcnt, maxseq, maxoccur);
fclose(out);
fclose(out2);
}
// ---------------- pepx_saveall ---------------------
void pepx_saveall()
{
int i;
char fname[LINELEN];
for(i = mINPEPSIZE; i <= mAXPEPSIZE; i++)
{
if(!IL_merge)
sprintf(fname, "%s/pepx%d.idx", indexfolder, i);
else
sprintf(fname, "%s/pepxIL%d.idx", indexfolder, i);
pepx_save(fname, i);
}
}
/******* rescompare **************************************************/
int rescompare (char *str1, char *str2)
{
return (strncmp(str1, str2, ACLEN));
}
/******* pepcompare **************************************************/
int pepcompare (char *str1, char *str2)
{
fseek(currentindex, (long)str2, 0);
fgets(currentresult, 32, currentindex);
//fprintf(stderr,"current idx2 file pos: %li, fseek returned %d\n",(int)str2,fret);
//fprintf(stderr,"res: %s\n",currentresult);
return (strncmp(str1, currentresult, currentpepsize));
}
// ---------------- pepx_reportnomatch ---------------------
int pepx_reportnomatch(char *orgquerystring)
{
//fprintf(stdout,"NO_MATCH %s\n", outputmode);
if(json)
fprintf(stdout, "]\n}"); // close empty entrymatches
else
fprintf(stdout, "\nNO_MATCH %s%s", orgquerystring, linesep);
return(0);
}
// ---------------- pepx_merge_with_prev_res ---------------------
int pepx_merge_with_prev_res(char endres[MAXSEQ][ACLEN + 4], char curres[MAXSEQ][ACLEN], char *acstr, int rescnt)
{
char isoonly[ACLEN], isovar[ACLEN] = "", prevmatch[ACLEN] = "", *dashptr, *matchptr;
int i, j, prevmatchvar, dupcnt = 0;
//fprintf(stderr,"acstring: %s\n",acstr);
j = rescnt;
if(strlen(acstr) == 0)
// first pep of a query
{
//fprintf(stderr,"\nfirst 6-mer: %d hits\n",j);
for(i = 0; i < rescnt; i++)
{
if(i && !strcmp(curres[i], curres[i - 1]))
{
dupcnt++;
continue; // fprintf(stderr,"\ndup: %s\n",curres[i]);, TODO: investigate why it occurs, eg: ASQSIS
}
//fprintf(stderr,"%d: %s (dupcnt: %d)\n",i,curres[i],dupcnt);
strcpy(endres[i], curres[i]);
strcat(acstr, curres[i]);
strcat(acstr, ",");
}
j = rescnt - dupcnt;
}
else // Check the match did exist for previous peps
{
for(i = j = 0; i < rescnt; i++)
{
strcpy(isoonly, curres[i]);
if((dashptr = strrchr(isoonly, '-')) != isoonly + 6)
// Remove variant pos before searching prev results
{
//fprintf(stderr,"removing varpos for %s\n",isoonly);
strcpy(isovar, isoonly);
//fprintf(stderr,"isovar now: %s\n",isovar);
*dashptr = 0;
}
//fprintf(stderr,"checking %s (result %d/%d)\n",curres[i],i+1,rescnt);
if(matchptr = strstr(acstr, curres[i]))
for(; matchptr; matchptr = strstr(matchptr + 1, curres[i]))
{
strncpy(prevmatch, matchptr, ACLEN);
*strchr(prevmatch, ',') = 0;
if((dashptr = strrchr(prevmatch, '-')) != prevmatch + 6)
prevmatchvar = TRUE;
else
prevmatchvar = FALSE;
//fprintf(stderr,"prevmatchvar: %d\n",prevmatchvar);
if(!strcmp(prevmatch, curres[i]) || (prevmatchvar && strstr(prevmatch, curres[i])))
// If a new match without variant falls on a previous match with variant: keep variant
{
//fprintf(stderr,"keeping prevmatch: %s\n",prevmatch);
strcpy(endres[j++], prevmatch);
}
//else fprintf(stderr,"discarding prevmatch: %s\n",prevmatch);
}
else if (isovar && (matchptr = strstr(acstr, isoonly)))
// new match is a variant
{
strncpy(prevmatch, matchptr, ACLEN);
*strchr(prevmatch, ',') = 0;
//fprintf(stderr,"isovar: %s, prevmatch: %s\n",isovar,prevmatch);
if(strrchr(prevmatch, '-') == prevmatch + 6)
// replace simple match by new variant match
strcpy(endres[j++], isovar);
else if(strstr(prevmatch, isoonly))
// reconduct previous variant pos
strcpy(endres[j++], prevmatch);
//else fprintf(stderr,"%s not added to endres\n\n",isovar);
}
*isovar = 0;
}
if(j)
// regenerate actring
{
//fprintf(stderr,"j equals %d, regenerating ACstring\n",j);
*acstr = 0;
for(i = 0; i < j; i++)
{
strcat(acstr, endres[i]);
strcat(acstr, ",");
}
//fprintf(stderr,"regenerated ACstring: %s\n\n",acstr);
}
}
return(j);
}
// ---------------- pepx_search ---------------------
int pepx_search(char *query, IDXDATA *idx)
{
typedef char actab[ACLEN];
int i, j, jpos = -1, jcnt = 0, found, rescnt = 0, pepsize, fpos;
char querystring[MAXPEPSIZE], ac[ACLEN], newquery[MAXPEPSIZE], fname[LINELEN], buf[MAXPEPSIZE + 1], *ptr;
char acholder[ACLEN + 1], jokerAA;
actab *currentresults;
FILE *ffh;
strcpy(querystring, query);
pepsize = strlen(query);
if(pepsize < mINPEPSIZE) // eg: six AA peptide with 7-mer indexes
{
strcat(querystring,"X"); // add a trailing joker to match index size
pepsize++;
}
currentpepsize = pepsize;
currentindex = idx[pepsize].fh;
currentresults = results;
for(i = 0; i < pepsize; i++)
if(querystring[i] == 'X')
{
jpos = i;
jcnt++;
}
else if(IL_merge && (querystring[i] == 'I' || querystring[i] == 'L'))
// We are querying against the IL_merged index
querystring[i] = 'J';
if(jcnt > 1)
// too many jokers
{
fprintf(stderr, "\n%s: No more than 1 joker/6AA\n", query);
return(0);
}
else if(jcnt == 1) // we have one joker
{
for(i = 0; i < strlen(aarevcode); i++)
// For each of the 20 AAs, or 19 if in ILmode
{
memset(newquery, 0, mAXPEPSIZE);
strncpy(newquery, querystring, jpos);
jokerAA = aarevcode[i];
if(IL_merge && jokerAA == 'I') // skip this one
continue;
if(IL_merge && jokerAA == 'L')
jokerAA = 'J';
strncat(newquery, &jokerAA, 1); // append single char joker
strcat(newquery, querystring + jpos + 1);
//fprintf(stderr,"\nnewquery: %s\n",newquery);
if(bsearch(newquery, NULL, idx[pepsize].elemcnt, pepsize + INDEX2WIDTH, pepcompare))
{
fpos = atoi(currentresult + pepsize);
ffh = idx[pepsize].ffh;
fseek(ffh, fpos, SEEK_SET);
// skip peptide
fgets(ac, ACLEN, ffh); // read matched peptide
while(fgets(ac, ACLEN, ffh))
// get all ACs
{
if(strlen(ac) > MAXPEPSIZE + 1) // We're still an accession
{
if(ptr = strrchr(ac, '\n'))
* ptr = 0;
else // max len identifiere eg:Q8WZ42-11-11658
ac[ACLEN - 1] = 0;
// make results uniques
for(found = FALSE, j = 0; j < rescnt; j++)
if(!strcmp(ac, currentresults[j]))
{
found = TRUE;
break;
}
if(!found) // TODO: Investigate why it doesn't work 100%, there are still duplicate variants in results when using a joker (eg: HTXEKPY)
strcpy(currentresults[rescnt++], ac);
}
else
break; // We've reached the next peptide
}
}
}
return(rescnt);
}
// No jokers
if(!bsearch(querystring, NULL, idx[pepsize].elemcnt, pepsize + INDEX2WIDTH, pepcompare))
// No match
{
//fprintf(stderr,"\n%s: not found in %s\n",querystring,idx==idxinfoIL?"ILindex":"BaseIndex");
return(0);
}
//fprintf(stderr,"\n%s: found in %s\n",querystring,idx==idxinfoIL?"ILindex":"BaseIndex");
fpos = atoi(currentresult + pepsize);
ffh = idx[pepsize].ffh;
fseek(ffh, fpos, SEEK_SET);
// skip peptide
fgets(ac, ACLEN, ffh);
//fprintf(stderr,"\nReading match ACs for %s\n",ac);
while(fgets(acholder, ACLEN + 1, ffh))
// get all ACs
{
strncpy(ac, acholder, ACLEN);
if(strlen(ac) > MAXPEPSIZE + 1)
{
if(ptr = strrchr(ac, '\n'))
* ptr = 0;
else // max len identifiere eg:Q8WZ42-11-11658
ac[ACLEN - 1] = 0;
//fprintf(stderr,"\nrescnt %d %s: %s(%d)\n",rescnt, query,ac,strlen(ac));
strcpy(currentresults[rescnt++], ac);
}
else
{
//fprintf(stderr,"\nBreaking at %s\n",ac);
break;
}
}
//fprintf(stderr,"\nReturning %d matches\n",rescnt);
return(rescnt);
}
int is10digits(char *match)
{
if(match[0] == 'P' && isalpha(match[1]))
/*if(!strncmp(match,"PA",2) || !strncmp(match,"PB",2) || !strncmp(match,"PC",2) ||
!strncmp(match,"PD",2) || !strncmp(match,"PE",2) || !strncmp(match,"PF",2) ||
!strncmp(match,"PG",2) || !strncmp(match,"PH",2) || !strncmp(match,"PI",2)) */
return(1);
return(0);
}
// ---------------- pepx_displaymatches ---------------------
void pepx_displaymatches(char matches[][ACLEN + 4] , int nbmatch, char *orgquerystring, char *querystring)
// orgquerystring the original modified or commented peptide (GCS*PLKKT*V), querystring the peptide stripped on non AA characters
{
int ac_cnt, i;
char ac[ACLEN], lastac[ACLEN] = "";
// Sort results by AC
if(nbmatch > 2)
qsort(matches, nbmatch, ACLEN + 4, rescompare);
if(!strcmp(matchmode, "ACONLY"))
// Re-filter without iso ids (it is already sorted)
{
ac_cnt = 0;
for(i = 0; i < nbmatch; i++)
{
if(!strchr(matches[i], '-'))
// it can happen at pos 0, eg: VIDLT, to investigate
{
//fprintf(stderr,"No dash at %d %s\n",i,ac);
continue;
}
strcpy(ac, matches[i]);
*strchr(ac, '-') = 0;
if(strcmp(ac, lastac))
strcpy(results[ac_cnt++], ac);
strcpy(lastac, ac);
}
// re-fill final results
nbmatch = ac_cnt;
for(i = 0; i < nbmatch; i++)
strcpy(matches[i], results[i]);
}
if(!strcmp(outputmode, "BATCH"))
// input from file (results are comma-separated)
{
//printf(stdout,"\n");
if(nbmatch == 0)
fprintf(stdout, "NO_MATCH");
else for(i = 0; i < nbmatch; i++)
{
// Check for coded 10-digit ACs
fprintf(stdout, "%s", is10digits(matches[i]) ? code4tenAA(matches[i]) : matches[i]);
if(i != nbmatch - 1)
fprintf(stdout, ","); // match separator
}
// Reminder of the query
fprintf(stdout, " %s\n", orgquerystring);
}
else
{
// input from stdin or envstring in web cgi mode (results are crlf-separated)
//fprintf(stdout,"\n%s: %d match(s)%s",querystring,cnt,linesep);
if(!json)
fprintf(stdout, "%s%s: %d match(s)%s", linesep, querystring, nbmatch, linesep);
for(i = 0; i < nbmatch; i++)
{
if(json)
{
strcpy(ac, matches[i]);
*strchr(ac, '-') = 0;
if(strcmp(ac, lastac))
{
if(i)
// close previous iso and entrymatch tag
fprintf(stdout, "]\n},");
if(is10digits(ac)) // Check for coded 10-digit ACs
fprintf(stdout, "{\n\"entryName\":\"%s\",\n\"isoforms\":[", code4tenAA(ac));
else
fprintf(stdout, "{\n\"entryName\":\"%s\",\n\"isoforms\":[", ac);
strcpy(lastac, ac);
}
else fprintf(stdout, ",");
if(is10digits(ac))
fprintf(stdout, "%s", pepx_tojson(code4tenAA(matches[i])));
else
fprintf(stdout, "%s", pepx_tojson(matches[i]));
}
else fprintf(stdout, "%s%s", is10digits(matches[i]) ? code4tenAA(matches[i]) : matches[i], linesep);
}
if(json)
fprintf(stdout, "]\n}\n]\n}\n"); // finished, close iso and entrymatch tags tags
else
fprintf(stdout, "%s: %d match(s)%s", querystring, nbmatch, linesep);
}
}
// ---------------- pepx_filterquery ---------------------
int pepx_filterquery(char *query, char *querystring)
{
char *qptr;
int i;
for(i = 0, qptr = querystring; i < strlen(query); i++)
{
// uppercase
query[i] = toupper(query[i]);
if(!strchr(aarevcode, query[i]))
{
if(isspace(query[i]) || isdigit(query[i])
|| (query[i] == '*')
|| (query[i] == '#')
|| (query[i] == '.')
|| (query[i] == '(')
|| (query[i] == ')'))
// just don't copy unwanted, and allow to keep eventually tagged seq for result display
i = i;
else if((query[i] == 'X') || (query[i] == 'J' && IL_merge))
// This is OK
*qptr++ = query[i];
else
{
// Todo: Maybe consider U as C
fprintf(stderr, "\n%c is not an AA\n", query[i]);
return(0);
}
}
else
*qptr++ = query[i];
}
*qptr = 0;
return(1);
}
// ---------------- pepx_processquery ---------------------
int pepx_processquery(char *orgquerystring)
{
char query[8192], querystring[8192], nextquery[8192], subquery[MAXPEPSIZE + 1] = "", acstring[400000] = "", finalres[MAXSEQ][ACLEN + 4];
char *qptr;
int row = 0, i, j, cnt;
// TODO: rewrite and iterate one by one AA, or 1rst and last and one by one ?
strcpy(query, orgquerystring);
if(json) fprintf(stdout, "{\n\"peptide\":\"%s\",\n\"entryMatches\":[", query);
if(!strcmp(outputmode, "BATCH"))
// Only first token is the peptide
{
for(i = 0; i < strlen(query); i++)
if(isspace(query[i]))
{
query[i] = 0;
break;
}
}
// quick filter
if(!pepx_filterquery(query, querystring))
// invalid query
return(0);
strcpy(query, querystring);
//if(strlen(query) >= 4096) {strncpy(subquery,query,12); subquery[12] = 0; fprintf(stderr,"\nQuery length: %d %s...\n",strlen(query),subquery);}
while(strlen(query) > mAXPEPSIZE)
{
// Split query in overlaping subqueries of maximum length
//fprintf(stderr,"pepx_processquery filtered query: %s, copying %d AAs in subquery\n",query,MAXPEPSIZE);
strncpy(subquery, query, mAXPEPSIZE);
subquery[mAXPEPSIZE] = 0;
//fprintf(stderr,"pepx_processquery subquery %s\n",subquery);
//strcpy(nextquery, query + mAXPEPSIZE - 1); // Faster but more false pos
// Prepare next subquery
if(strlen(querystring) > 25)
strcpy(nextquery,query + MAXPEPSIZE-1); // Faster but more false pos
else if(strlen(querystring) > 16)
strcpy(nextquery,query + 2);
else
strcpy(nextquery,query + 1);
strcpy(query, nextquery);
//fprintf(stderr,"will look for %s\n",query);
if(IL_merge)
cnt = pepx_search(subquery, idxinfoIL);
else
cnt = pepx_search(subquery, idxinfo);
if(cnt == 0)
{
//fprintf(stderr,"pepx_processquery: no match for subquery %s\n",subquery);
return(pepx_reportnomatch(orgquerystring));
}
if((cnt = pepx_merge_with_prev_res(finalres, results, acstring, cnt) == 0))
return(pepx_reportnomatch(orgquerystring));
}
//fprintf(stderr,"pepx_processquery last complete subquery OK\n");
if(i = strlen(query)) // otherwise we're finished
{
//fprintf(stderr,"pepx_processquery query not finished, prepare next subquery\n");
if(strlen(subquery)) // issue last subquery with the longest remaining x-mer