int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq; AjPTable table = 0; AjPFile outf; ajint wordsize; ajint mincount; embInit("wordcount", argc, argv); seqall = ajAcdGetSeqall("sequence1"); wordsize = ajAcdGetInt("wordsize"); outf = ajAcdGetOutfile("outfile"); mincount = ajAcdGetInt("mincount"); embWordLength(wordsize); while (ajSeqallNext(seqall, &seq)) { embWordGetTable(&table, seq); /* get table of words */ } embWordPrintTableFI(table, mincount, outf); /* print table of words */ /* ** test if table can be added to ** if(getWordTable(&table, seq, wordcount)) ?? get table of words ?? ** { ** printWordTable(table); ?? print table of words ?? ** } */ embWordFreeTable(&table); /* free table of words */ ajSeqallDel(&seqall); ajSeqDel(&seq); ajFileClose(&outf); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seq1; AjPSeqset seq2; AjPSeq a; const AjPSeq b; AjPStr m = 0; AjPStr n = 0; AjPFile errorf; AjBool show = ajFalse; ajint lena = 0; ajint lenb = 0; const char *p; const char *q; AjPMatrixf matrix; AjPSeqCvt cvt = 0; float **sub; ajint *compass = NULL; float *path = NULL; float gapopen; float gapextend; float score; ajint begina; ajint i; ajuint k; ajint beginb; ajint start1 = 0; ajint start2 = 0; ajint end1 = 0; ajint end2 = 0; ajint width = 0; AjPTable seq1MatchTable = 0; ajint wordlen = 6; ajint oldmax = 0; AjPAlign align = NULL; embInit("supermatcher", argc, argv); matrix = ajAcdGetMatrixf("datafile"); seq1 = ajAcdGetSeqall("asequence"); seq2 = ajAcdGetSeqset("bsequence"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); wordlen = ajAcdGetInt("wordlen"); align = ajAcdGetAlign("outfile"); errorf = ajAcdGetOutfile("errorfile"); width = ajAcdGetInt("width"); /* not the same as awidth */ gapopen = ajRoundFloat(gapopen, 8); gapextend = ajRoundFloat(gapextend, 8); sub = ajMatrixfGetMatrix(matrix); cvt = ajMatrixfGetCvt(matrix); embWordLength(wordlen); ajSeqsetTrim(seq2); while(ajSeqallNext(seq1,&a)) { ajSeqTrim(a); begina = 1 + ajSeqGetOffset(a); m = ajStrNewRes(1+ajSeqGetLen(a)); lena = ajSeqGetLen(a); ajDebug("Read '%S'\n", ajSeqGetNameS(a)); if(!embWordGetTable(&seq1MatchTable, a)) /* get table of words */ ajErr("Could not generate table for %s\n", ajSeqGetNameC(a)); for(k=0;k<ajSeqsetGetSize(seq2);k++) { b = ajSeqsetGetseqSeq(seq2, k); lenb = ajSeqGetLen(b); beginb = 1 + ajSeqGetOffset(b); ajDebug("Processing '%S'\n", ajSeqGetNameS(b)); p = ajSeqGetSeqC(a); q = ajSeqGetSeqC(b); if(!supermatcher_findstartpoints(seq1MatchTable,b,a, &start1, &start2, &end1, &end2)) { ajFmtPrintF(errorf, "No wordmatch start points for " "%s vs %s. No alignment\n", ajSeqGetNameC(a),ajSeqGetNameC(b)); continue; } n=ajStrNewRes(1+ajSeqGetLen(b)); ajStrAssignC(&m,""); ajStrAssignC(&n,""); ajDebug("++ %S v %S start:%d %d end:%d %d\n", ajSeqGetNameS(a), ajSeqGetNameS(b), start1, start2, end1, end2); if(end1-start1+1 > oldmax) { oldmax = ((end1-start1)+1); AJRESIZE(path,oldmax*width*sizeof(float)); AJRESIZE(compass,oldmax*width*sizeof(ajint)); ajDebug("++ resize to oldmax: %d\n", oldmax); } for(i=0;i<((end1-start1)+1)*width;i++) path[i] = 0.0; ajDebug("Calling embAlignPathCalcFast " "%d..%d [%d/%d] %d..%d [%d/%d]\n", start1, end1, (end1 - start1 + 1), lena, start2, end2, (end2 - start2 + 1), lenb); score = embAlignPathCalcSWFast(&p[start1],&q[start2], end1-start1+1,end2-start2+1, 0,width, gapopen,gapextend, path,sub,cvt, compass,show); embAlignWalkSWMatrixFast(path,compass,gapopen,gapextend,a,b, &m,&n,end1-start1+1,end2-start2+1, 0,width, &start1,&start2); if(!ajAlignFormatShowsSequences(align)) { ajAlignDefineCC(align, ajStrGetPtr(m), ajStrGetPtr(n), ajSeqGetNameC(a), ajSeqGetNameC(b)); ajAlignSetScoreR(align, score); } else { embAlignReportLocal(align, a, b, m,n,start1,start2, gapopen, gapextend, score,matrix, begina, beginb); } ajAlignWrite(align); ajAlignReset(align); ajStrDel(&n); } embWordFreeTable(&seq1MatchTable); /* free table of words */ seq1MatchTable=0; ajStrDel(&m); } if(!ajAlignFormatShowsSequences(align)) { ajMatrixfDel(&matrix); } AJFREE(path); AJFREE(compass); ajAlignClose(align); ajAlignDel(&align); ajSeqallDel(&seq1); ajSeqDel(&a); ajSeqsetDel(&seq2); ajFileClose(&errorf); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeq seq1; AjPSeq seq2; ajint wordlen; AjPTable seq1MatchTable = 0; AjPList matchlist = NULL; AjPGraph graph = NULL; AjPGraph xygraph = NULL; AjBool boxit; /* ** Different ticks as they need to be different for x and y due to ** length of string being important on x */ ajuint acceptableticksx[]= { 1,10,50,100,500,1000,1500,10000, 500000,1000000,5000000 }; ajuint acceptableticks[]= { 1,10,50,100,200,500,1000,2000,5000,10000,15000, 500000,1000000,5000000 }; ajint numbofticks = 10; float xmargin; float ymargin; float ticklen; float tickgap; float onefifth = 0.0; ajint i; float k; float max; char ptr[10]; ajint begin1; ajint begin2; ajint end1; ajint end2; ajuint len1; ajuint len2; float fbegin1; float fbegin2; float fend1; float fend2; float flen1; float flen2; AjBool stretch; embInit("dottup", argc, argv); wordlen = ajAcdGetInt("wordsize"); seq1 = ajAcdGetSeq("asequence"); seq2 = ajAcdGetSeq("bsequence"); graph = ajAcdGetGraph("graph"); boxit = ajAcdGetBoolean("boxit"); stretch = ajAcdGetToggle("stretch"); xygraph = ajAcdGetGraphxy("xygraph"); begin1 = ajSeqGetBegin(seq1); begin2 = ajSeqGetBegin(seq2); end1 = ajSeqGetEnd(seq1); end2 = ajSeqGetEnd(seq2); len1 = end1 - begin1 + 1; len2 = end2 - begin2 + 1; flen1 = (float) len1; flen2 = (float) len2; fbegin1 = (float) begin1; fbegin2 = (float) begin2; fend1 = (float) end1; fend2 = (float) end2; offset1 = fbegin1; offset2 = fbegin2; ajSeqTrim(seq1); ajSeqTrim(seq2); embWordLength(wordlen); if(embWordGetTable(&seq1MatchTable, seq1)) matchlist = embWordBuildMatchTable(seq1MatchTable, seq2, ajTrue); if(stretch) { dottup_stretchplot(xygraph,matchlist,seq1,seq2,begin1,begin2,end1, end2); if(matchlist) embWordMatchListDelete(&matchlist); /* free the match structures */ } else { /* only here if stretch is false */ max= flen1; if(flen2 > max) max = flen2; xmargin = ymargin = max * (float)0.15; ajGraphOpenWin(graph, fbegin1-ymargin,fend1+ymargin, fbegin2-xmargin,(float)fend2+xmargin); ajGraphicsSetCharscale(0.5); if(matchlist) dottup_plotMatches(matchlist); if(boxit) { ajGraphicsDrawposRect(fbegin1, fbegin2, fend1, fend2); i = 0; while(acceptableticksx[i]*numbofticks < len1) i++; if(i<=13) tickgap = (float) acceptableticksx[i]; else tickgap = (float) acceptableticksx[10]; ticklen = xmargin * (float) 0.1; onefifth = xmargin * (float)0.2; ajGraphicsDrawposTextAtmid(fbegin1+flen1*(float)0.5, fbegin1-(onefifth*(float)3.0), ajGraphGetYlabelC(graph)); if(len2/len1 > 10 ) { /* a lot smaller then just label start and end */ ajGraphicsDrawposLine(fbegin1,fbegin2,fbegin1, fbegin2-ticklen); sprintf(ptr,"%u",ajSeqGetOffset(seq1)); ajGraphicsDrawposTextAtmid(fbegin1,fbegin2-(onefifth),ptr); ajGraphicsDrawposLine(fend1,fbegin2, fend1,fbegin2-ticklen); sprintf(ptr,"%d",end1); ajGraphicsDrawposTextAtmid(fend1,fbegin2-(onefifth),ptr); } else for(k=fbegin1;k<fend1;k+=tickgap) { ajGraphicsDrawposLine(k,fbegin2,k,fbegin2-ticklen); sprintf(ptr,"%d",(ajint)k); ajGraphicsDrawposTextAtmid( k,fbegin2-(onefifth),ptr); } i = 0; while(acceptableticks[i]*numbofticks < len2) i++; tickgap = (float) acceptableticks[i]; ticklen = ymargin*(float)0.1; onefifth = ymargin*(float)0.2; ajGraphicsDrawposTextAtlineJustify(fbegin1-(onefifth*(float)4.), fbegin2+flen2*(float)0.5, fbegin2-(onefifth*(float)4.), fbegin2+flen2, ajGraphGetXlabelC(graph), 0.5); if(len1/len2 > 10 ) { /* a lot smaller then just label start and end */ ajGraphicsDrawposLine(fbegin1,fbegin2,fbegin1-ticklen, fbegin2); sprintf(ptr,"%u",ajSeqGetOffset(seq2)); ajGraphicsDrawposTextAtend(fbegin1-(onefifth),fbegin2,ptr); ajGraphicsDrawposLine(fbegin1,fend2,fbegin1-ticklen, fend2); sprintf(ptr,"%d",end2); ajGraphicsDrawposTextAtend(fbegin2-(onefifth),fend2,ptr); } else for(k=fbegin2;k<fend2;k+=tickgap) { ajGraphicsDrawposLine(fbegin1,k,fbegin1-ticklen,k); sprintf(ptr,"%d",(ajint)k); ajGraphicsDrawposTextAtend(fbegin1-(onefifth),k,ptr); } } } ajGraphicsClose(); ajSeqDel(&seq1); ajSeqDel(&seq2); ajGraphxyDel(&graph); ajGraphxyDel(&xygraph); embWordFreeTable(&seq1MatchTable); if(matchlist) embWordMatchListDelete(&matchlist); /* free the match structures */ embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqset seqset; const AjPSeq seq1; const AjPSeq seq2; ajint wordlen; AjPTable seq1MatchTable = NULL; AjPList matchlist ; AjPGraph graph = 0; ajuint i; ajuint j; float total=0; ajuint acceptableticks[]= { 1,10,50,100,200,500,1000,1500,10000,50000, 100000,500000,1000000,5000000 }; ajint numbofticks = 10; ajint gap,tickgap; AjBool boxit = AJTRUE; AjBool dumpfeat = AJFALSE; float xmargin; float ymargin; float k; char ptr[10]; float ticklen; float onefifth; AjPFeattable *tabptr = NULL; AjPFeattabOut seq1out = NULL; AjPStr sajb = NULL; float flen1; float flen2; ajuint tui; embInit("polydot", argc, argv); wordlen = ajAcdGetInt("wordsize"); seqset = ajAcdGetSeqset("sequences"); graph = ajAcdGetGraph("graph"); gap = ajAcdGetInt("gap"); boxit = ajAcdGetBoolean("boxit"); seq1out = ajAcdGetFeatout("outfeat"); dumpfeat = ajAcdGetToggle("dumpfeat"); sajb = ajStrNew(); embWordLength(wordlen); AJCNEW(lines,ajSeqsetGetSize(seqset)); AJCNEW(pts,ajSeqsetGetSize(seqset)); AJCNEW(tabptr,ajSeqsetGetSize(seqset)); for(i=0;i<ajSeqsetGetSize(seqset);i++) { seq1 = ajSeqsetGetseqSeq(seqset, i); total += ajSeqGetLen(seq1); } total +=(float)(gap*(ajSeqsetGetSize(seqset)-1)); xmargin = total*(float)0.15; ymargin = total*(float)0.15; ticklen = xmargin*(float)0.1; onefifth = xmargin*(float)0.2; i = 0; while(acceptableticks[i]*numbofticks < ajSeqsetGetLen(seqset)) i++; if(i<=13) tickgap = acceptableticks[i]; else tickgap = acceptableticks[13]; ajGraphAppendTitleS(graph, ajSeqsetGetUsa(seqset)); ajGraphOpenWin(graph, (float)0.0-xmargin,(total+xmargin)*(float)1.35, (float)0.0-ymargin, total+ymargin); ajGraphicsSetCharscale((float)0.3); for(i=0;i<ajSeqsetGetSize(seqset);i++) { which = i; seq1 = ajSeqsetGetseqSeq(seqset, i); tui = ajSeqGetLen(seq1); flen1 = (float) tui; if(embWordGetTable(&seq1MatchTable, seq1)){ /* get table of words */ for(j=0;j<ajSeqsetGetSize(seqset);j++) { seq2 = ajSeqsetGetseqSeq(seqset, j); tui = ajSeqGetLen(seq2); flen2 = (float) tui; if(boxit) ajGraphicsDrawposRect(xstart,ystart, xstart+flen1, ystart+flen2); matchlist = embWordBuildMatchTable(seq1MatchTable, seq2, ajTrue); if(matchlist) polydot_plotMatches(matchlist); if(i<j && dumpfeat) embWordMatchListConvToFeat(matchlist,&tabptr[i], &tabptr[j],seq1, seq2); if(matchlist) /* free the match structures */ embWordMatchListDelete(&matchlist); if(j==0) { for(k=0.0;k<ajSeqGetLen(seq1);k+=tickgap) { ajGraphicsDrawposLine(xstart+k,ystart,xstart+k, ystart-ticklen); sprintf(ptr,"%d",(ajint)k); ajGraphicsDrawposTextAtmid(xstart+k, ystart-(onefifth), ptr); } ajGraphicsDrawposTextAtmid( xstart+(flen1/(float)2.0), ystart-(3*onefifth), ajStrGetPtr(ajSeqsetGetseqNameS(seqset, i))); } if(i==0) { for(k=0.0;k<ajSeqGetLen(seq2);k+=tickgap) { ajGraphicsDrawposLine(xstart,ystart+k,xstart-ticklen, ystart+k); sprintf(ptr,"%d",(ajint)k); ajGraphicsDrawposTextAtend(xstart-(onefifth), ystart+k, ptr); } ajGraphicsDrawposTextAtlineJustify( xstart-(3*onefifth), ystart+(flen2/(float)2.0), xstart-(3*onefifth),ystart+flen2, ajStrGetPtr(ajSeqsetGetseqNameS(seqset, j)),0.5); } ystart += flen2+(float)gap; } } embWordFreeTable(&seq1MatchTable); seq1MatchTable = NULL; xstart += flen1+(float)gap; ystart = 0.0; } ajGraphicsDrawposTextAtstart(total+onefifth,total-(onefifth), "No. Length Lines Points Sequence"); for(i=0;i<ajSeqsetGetSize(seqset);i++) { seq1 = ajSeqsetGetseqSeq(seqset, i); ajFmtPrintS(&sajb,"%3u %6d %5d %6d %s",i+1, ajSeqGetLen(seq1),lines[i], pts[i],ajSeqGetNameC(seq1)); ajGraphicsDrawposTextAtstart(total+onefifth,total-(onefifth*(i+2)), ajStrGetPtr(sajb)); } if(dumpfeat && seq1out) { for(i=0;i<ajSeqsetGetSize(seqset);i++) { ajFeattableWrite(seq1out, tabptr[i]); ajFeattableDel(&tabptr[i]); } } ajGraphicsClose(); ajGraphxyDel(&graph); ajStrDel(&sajb); AJFREE(lines); AJFREE(pts); AJFREE(tabptr); ajSeqsetDel(&seqset); ajFeattabOutDel(&seq1out);; embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall queryseqs; AjPSeqset targetseqs; AjPSeq queryseq; const AjPSeq targetseq; AjPStr queryaln = 0; AjPStr targetaln = 0; AjPFile errorf; AjBool show = ajFalse; const char *queryseqc; const char *targetseqc; AjPMatrixf matrix; AjPSeqCvt cvt = 0; float **sub; ajint *compass = NULL; float *path = NULL; float gapopen; float gapextend; float score; float minscore; ajuint j, k; ajint querystart = 0; ajint targetstart = 0; ajint queryend = 0; ajint targetend = 0; ajint width = 0; AjPTable kmers = 0; ajint wordlen = 6; ajint oldmax = 0; ajint newmax = 0; ajuint ntargetseqs; ajuint nkmers; AjPAlign align = NULL; EmbPWordMatch maxmatch; /* match with maximum score */ /* Cursors for the current sequence being scanned, ** i.e., until which location it was scanned. ** Separate cursor/location entries for each sequence in the seqset. */ ajuint* lastlocation; EmbPWordRK* wordsw = NULL; AjPList* matchlist = NULL; embInit("supermatcher", argc, argv); matrix = ajAcdGetMatrixf("datafile"); queryseqs = ajAcdGetSeqall("asequence"); targetseqs= ajAcdGetSeqset("bsequence"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); wordlen = ajAcdGetInt("wordlen"); align = ajAcdGetAlign("outfile"); errorf = ajAcdGetOutfile("errorfile"); width = ajAcdGetInt("width"); /* width for banded Smith-Waterman */ minscore = ajAcdGetFloat("minscore"); gapopen = ajRoundFloat(gapopen, 8); gapextend = ajRoundFloat(gapextend, 8); sub = ajMatrixfGetMatrix(matrix); cvt = ajMatrixfGetCvt(matrix); embWordLength(wordlen); /* seqset sequence is the reference sequence for SAM format */ ajAlignSetRefSeqIndx(align, 1); ajSeqsetTrim(targetseqs); ntargetseqs = ajSeqsetGetSize(targetseqs); AJCNEW0(matchlist, ntargetseqs); /* get tables of words */ for(k=0;k<ntargetseqs;k++) { targetseq = ajSeqsetGetseqSeq(targetseqs, k); embWordGetTable(&kmers, targetseq); ajDebug("Number of distinct kmers found so far: %d\n", ajTableGetLength(kmers)); } AJCNEW0(lastlocation, ntargetseqs); if(ajTableGetLength(kmers)<1) ajErr("no kmers found"); nkmers = embWordRabinKarpInit(kmers, &wordsw, wordlen, targetseqs); while(ajSeqallNext(queryseqs,&queryseq)) { ajSeqTrim(queryseq); queryaln = ajStrNewRes(1+ajSeqGetLen(queryseq)); ajDebug("Read '%S'\n", ajSeqGetNameS(queryseq)); for(k=0;k<ntargetseqs;k++) { lastlocation[k]=0; matchlist[k] = ajListstrNew(); } embWordRabinKarpSearch(ajSeqGetSeqS(queryseq), targetseqs, (const EmbPWordRK*)wordsw, wordlen, nkmers, matchlist, lastlocation, ajFalse); for(k=0;k<ajSeqsetGetSize(targetseqs);k++) { targetseq = ajSeqsetGetseqSeq(targetseqs, k); ajDebug("Processing '%S'\n", ajSeqGetNameS(targetseq)); if(ajListGetLength(matchlist[k])==0) { ajFmtPrintF(errorf, "No wordmatch start points for " "%s vs %s. No alignment\n", ajSeqGetNameC(queryseq),ajSeqGetNameC(targetseq)); embWordMatchListDelete(&matchlist[k]); continue; } /* only the maximum match is used as seed * (if there is more than one location with the maximum match * only the first one is used) * TODO: we should add a new option to make above limit optional */ maxmatch = embWordMatchFirstMax(matchlist[k]); supermatcher_findendpoints(maxmatch,targetseq, queryseq, &targetstart, &querystart, &targetend, &queryend); targetaln=ajStrNewRes(1+ajSeqGetLen(targetseq)); queryseqc = ajSeqGetSeqC(queryseq); targetseqc = ajSeqGetSeqC(targetseq); ajStrAssignC(&queryaln,""); ajStrAssignC(&targetaln,""); ajDebug("++ %S v %S start:%d %d end:%d %d\n", ajSeqGetNameS(targetseq), ajSeqGetNameS(queryseq), targetstart, querystart, targetend, queryend); newmax = (targetend-targetstart+2)*width; if(newmax > oldmax) { AJCRESIZE0(path,oldmax,newmax); AJCRESIZE0(compass,oldmax,newmax); oldmax=newmax; ajDebug("++ memory re/allocation for path/compass arrays" " to size: %d\n", newmax); } else { AJCSET0(path,newmax); AJCSET0(compass,newmax); } ajDebug("Calling embAlignPathCalcSWFast " "%d..%d [%d/%d] %d..%d [%d/%d] width:%d\n", querystart, queryend, (queryend - querystart + 1), ajSeqGetLen(queryseq), targetstart, targetend, (targetend - targetstart + 1), ajSeqGetLen(targetseq), width); score = embAlignPathCalcSWFast(&targetseqc[targetstart], &queryseqc[querystart], targetend-targetstart+1, queryend-querystart+1, 0,width, gapopen,gapextend, path,sub,cvt, compass,show); if(score>minscore) { embAlignWalkSWMatrixFast(path,compass,gapopen,gapextend, targetseq,queryseq, &targetaln,&queryaln, targetend-targetstart+1, queryend-querystart+1, 0,width, &targetstart,&querystart); if(!ajAlignFormatShowsSequences(align)) { ajAlignDefineCC(align, ajStrGetPtr(targetaln), ajStrGetPtr(queryaln), ajSeqGetNameC(targetseq), ajSeqGetNameC(queryseq)); ajAlignSetScoreR(align, score); } else { ajDebug(" queryaln:%S \ntargetaln:%S\n", queryaln,targetaln); embAlignReportLocal(align, queryseq, targetseq, queryaln, targetaln, querystart, targetstart, gapopen, gapextend, score, matrix, 1 + ajSeqGetOffset(queryseq), 1 + ajSeqGetOffset(targetseq) ); } ajAlignWrite(align); ajAlignReset(align); } ajStrDel(&targetaln); embWordMatchListDelete(&matchlist[k]); } ajStrDel(&queryaln); } for(k=0;k<nkmers;k++) { AJFREE(wordsw[k]->seqindxs); AJFREE(wordsw[k]->nSeqMatches); for(j=0;j<wordsw[k]->nseqs;j++) AJFREE(wordsw[k]->locs[j]); AJFREE(wordsw[k]->nnseqlocs); AJFREE(wordsw[k]->locs); AJFREE(wordsw[k]); } embWordFreeTable(&kmers); if(!ajAlignFormatShowsSequences(align)) ajMatrixfDel(&matrix); AJFREE(path); AJFREE(compass); AJFREE(kmers); AJFREE(wordsw); AJFREE(matchlist); AJFREE(lastlocation); ajAlignClose(align); ajAlignDel(&align); ajSeqallDel(&queryseqs); ajSeqDel(&queryseq); ajSeqsetDel(&targetseqs); ajFileClose(&errorf); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqset seqset; AjPSeqall seqall; AjPSeq queryseq; const AjPSeq targetseq; ajint wordlen; AjPTable wordsTable = NULL; AjPList* matchlist = NULL; AjPFile logfile; AjPFeattable* seqsetftables = NULL; AjPFeattable seqallseqftable = NULL; AjPFeattabOut ftoutforseqsetseq = NULL; AjPFeattabOut ftoutforseqallseq = NULL; AjPAlign align = NULL; AjIList iter = NULL; ajint targetstart; ajint querystart; ajint len; ajuint i, j; ajulong nAllMatches = 0; ajulong sumAllScore = 0; AjBool dumpAlign = ajTrue; AjBool dumpFeature = ajTrue; AjBool checkmode = ajFalse; EmbPWordRK* wordsw = NULL; ajuint npatterns = 0; ajuint seqsetsize; ajuint nmatches; ajuint* nmatchesseqset; ajuint* lastlocation; /* Cursors for Rabin-Karp search. */ /* Shows until what point the query sequence was * scanned for a pattern sequences in the seqset. */ char* paddedheader = NULL; const char* header; AjPStr padding; header = "Pattern %S #pat-sequences #all-matches avg-match-length\n"; padding = ajStrNew(); embInit("wordmatch", argc, argv); wordlen = ajAcdGetInt("wordsize"); seqset = ajAcdGetSeqset("asequence"); seqall = ajAcdGetSeqall("bsequence"); logfile = ajAcdGetOutfile("logfile"); dumpAlign = ajAcdGetToggle("dumpalign"); dumpFeature = ajAcdGetToggle("dumpfeat"); if(dumpAlign) { align = ajAcdGetAlign("outfile"); ajAlignSetExternal(align, ajTrue); } seqsetsize = ajSeqsetGetSize(seqset); ajSeqsetTrim(seqset); AJCNEW0(matchlist, seqsetsize); AJCNEW0(seqsetftables, seqsetsize); AJCNEW0(nmatchesseqset, seqsetsize); if (dumpFeature) { ftoutforseqsetseq = ajAcdGetFeatout("aoutfeat"); ftoutforseqallseq = ajAcdGetFeatout("boutfeat"); } checkmode = !dumpFeature && !dumpAlign; embWordLength(wordlen); ajFmtPrintF(logfile, "Small sequence/file for constructing" " target patterns: %S\n", ajSeqsetGetUsa(seqset)); ajFmtPrintF(logfile, "Large sequence/file to be scanned" " for patterns: %S\n", ajSeqallGetUsa(seqall)); ajFmtPrintF(logfile, "Number of sequences in the patterns file: %u\n", seqsetsize); ajFmtPrintF(logfile, "Pattern/word length: %u\n", wordlen); for(i=0;i<seqsetsize;i++) { targetseq = ajSeqsetGetseqSeq(seqset, i); embWordGetTable(&wordsTable, targetseq); } AJCNEW0(lastlocation, seqsetsize); if(ajTableGetLength(wordsTable)>0) { npatterns = embWordRabinKarpInit(wordsTable, &wordsw, wordlen, seqset); ajFmtPrintF(logfile, "Number of patterns/words found: %u\n", npatterns); while(ajSeqallNext(seqall,&queryseq)) { for(i=0;i<seqsetsize;i++) { lastlocation[i]=0; if (!checkmode) matchlist[i] = ajListstrNew(); } nmatches = embWordRabinKarpSearch( ajSeqGetSeqS(queryseq), seqset, (EmbPWordRK const *)wordsw, wordlen, npatterns, matchlist, lastlocation, checkmode); nAllMatches += nmatches; if (checkmode) continue; for(i=0;i<seqsetsize;i++) { if(ajListGetLength(matchlist[i])>0) { iter = ajListIterNewread(matchlist[i]) ; while(embWordMatchIter(iter, &targetstart, &querystart, &len, &targetseq)) { if(dumpAlign) { ajAlignDefineSS(align, targetseq, queryseq); ajAlignSetScoreI(align, len); /* ungapped alignment means same length * for both sequences */ ajAlignSetSubRange(align, targetstart, 1, len, ajSeqIsReversed(targetseq), ajSeqGetLen(targetseq), querystart, 1, len, ajSeqIsReversed(queryseq), ajSeqGetLen(queryseq)); } } if(dumpAlign) { ajAlignWrite(align); ajAlignReset(align); } if(ajListGetLength(matchlist[i])>0 && dumpFeature) { embWordMatchListConvToFeat(matchlist[i], &seqsetftables[i], &seqallseqftable, targetseq, queryseq); ajFeattableWrite(ftoutforseqallseq, seqallseqftable); ajFeattableDel(&seqallseqftable); } ajListIterDel(&iter); } embWordMatchListDelete(&matchlist[i]); } } /* search completed, now report statistics */ for(i=0;i<npatterns;i++) { sumAllScore += wordsw[i]->lenMatches; for(j=0;j<wordsw[i]->nseqs;j++) nmatchesseqset[wordsw[i]->seqindxs[j]] += wordsw[i]->nSeqMatches[j]; } ajFmtPrintF(logfile, "Number of sequences in the file scanned " "for patterns: %u\n", ajSeqallGetCount(seqall)); ajFmtPrintF(logfile, "Number of all matches: %Lu" " (wordmatch finds exact matches only)\n", nAllMatches); if(nAllMatches>0) { ajFmtPrintF(logfile, "Sum of match lengths: %Lu\n", sumAllScore); ajFmtPrintF(logfile, "Average match length: %.2f\n", sumAllScore*1.0/nAllMatches); ajFmtPrintF(logfile, "\nDistribution of the matches among pattern" " sequences:\n"); ajFmtPrintF(logfile, "-----------------------------------------" "-----------\n"); for(i=0;i<ajSeqsetGetSize(seqset);i++) { if (nmatchesseqset[i]>0) ajFmtPrintF(logfile, "%-42s: %8u\n", ajSeqGetNameC(ajSeqsetGetseqSeq(seqset, i)), nmatchesseqset[i]); ajFeattableWrite(ftoutforseqsetseq, seqsetftables[i]); ajFeattableDel(&seqsetftables[i]); } ajFmtPrintF(logfile, "\nPattern statistics:\n"); ajFmtPrintF(logfile, "-------------------\n"); if(wordlen>7) ajStrAppendCountK(&padding, ' ', wordlen-7); paddedheader = ajFmtString(header,padding); ajFmtPrintF(logfile, paddedheader); for(i=0;i<npatterns;i++) if (wordsw[i]->nMatches>0) ajFmtPrintF(logfile, "%-7s: %12u %12u %17.2f\n", wordsw[i]->word->fword, wordsw[i]->nseqs, wordsw[i]->nMatches, wordsw[i]->lenMatches*1.0/wordsw[i]->nMatches); } } for(i=0;i<npatterns;i++) { for(j=0;j<wordsw[i]->nseqs;j++) AJFREE(wordsw[i]->locs[j]); AJFREE(wordsw[i]->locs); AJFREE(wordsw[i]->seqindxs); AJFREE(wordsw[i]->nnseqlocs); AJFREE(wordsw[i]->nSeqMatches); AJFREE(wordsw[i]); } embWordFreeTable(&wordsTable); AJFREE(wordsw); AJFREE(matchlist); AJFREE(lastlocation); AJFREE(nmatchesseqset); AJFREE(seqsetftables); if(dumpAlign) { ajAlignClose(align); ajAlignDel(&align); } if(dumpFeature) { ajFeattabOutDel(&ftoutforseqsetseq); ajFeattabOutDel(&ftoutforseqallseq); } ajFileClose(&logfile); ajSeqallDel(&seqall); ajSeqsetDel(&seqset); ajSeqDel(&queryseq); ajStrDel(&padding); AJFREE(paddedheader); embExit(); return 0; }