int main(int argc, char **argv) { AjPAlign align; AjPSeq a; AjPSeq b; AjPSeqout seqout; AjPStr m; AjPStr n; AjPStr merged = NULL; ajuint lena; ajuint lenb; const char *p; const char *q; ajint start1 = 0; ajint start2 = 0; float *path; ajint *compass; AjPMatrixf matrix; AjPSeqCvt cvt = 0; float **sub; float gapopen; float gapextend; ajulong maxarr = 1000; ajulong len; /* arbitrary. realloc'd if needed */ size_t stlen; float score; ajint begina; ajint beginb; embInit("merger", argc, argv); a = ajAcdGetSeq("asequence"); b = ajAcdGetSeq("bsequence"); seqout = ajAcdGetSeqout("outseq"); matrix = ajAcdGetMatrixf("datafile"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); align = ajAcdGetAlign("outfile"); gapopen = ajRoundFloat(gapopen, 8); gapextend = ajRoundFloat(gapextend, 8); AJCNEW(path, maxarr); AJCNEW(compass, maxarr); /* ** make the two sequences lowercase so we can show which one we are ** using in the merge by uppercasing it */ ajSeqFmtLower(a); ajSeqFmtLower(b); m = ajStrNew(); n = ajStrNew(); sub = ajMatrixfGetMatrix(matrix); cvt = ajMatrixfGetCvt(matrix); begina = ajSeqGetBegin(a); beginb = ajSeqGetBegin(b); lena = ajSeqGetLen(a); lenb = ajSeqGetLen(b); if(lenb > (ULONG_MAX/(ajulong)(lena+1))) ajFatal("Sequences too big. Try 'supermatcher'"); len = lena*lenb; if(len>maxarr) { ajDebug("merger: resize path, len to %d (%d * $d)\n", len, lena, lenb); stlen = (size_t) len; AJCRESIZE(path,stlen); AJCRESIZE(compass,stlen); maxarr=len; } p = ajSeqGetSeqC(a); q = ajSeqGetSeqC(b); ajStrAssignC(&m,""); ajStrAssignC(&n,""); score = embAlignPathCalc(p,q,lena,lenb,gapopen,gapextend,path,sub,cvt, compass, ajFalse); /*score = embAlignScoreNWMatrix(path,compass,gapopen,gapextend, a,b,lena,lenb,sub,cvt, &start1,&start2);*/ embAlignWalkNWMatrix(path,a,b,&m,&n,lena,lenb, &start1,&start2,gapopen, gapextend,compass); /* ** now construct the merged sequence, uppercase the bits of the two ** input sequences which are used in the merger */ merger_Merge(align, &merged,p,q,m,n,start1,start2, ajSeqGetNameC(a),ajSeqGetNameC(b)); embAlignReportGlobal(align, a, b, m, n, start1, start2, gapopen, gapextend, score, matrix, begina, beginb); ajAlignWrite(align); ajAlignReset(align); /* write the merged sequence */ ajSeqAssignSeqS(a, merged); ajSeqoutWriteSeq(seqout, a); ajSeqoutClose(seqout); ajSeqoutDel(&seqout); ajSeqDel(&a); ajSeqDel(&b); ajAlignClose(align); ajAlignDel(&align); ajStrDel(&merged); AJFREE(compass); AJFREE(path); ajStrDel(&n); ajStrDel(&m); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seqall; AjPSeqout seqout; AjPSeq seq; ajint before; ajint after; AjBool join; AjPFeattable featab; AjBool featinname; AjPStr describe; /* feature filter criteria */ AjPStr source = NULL; AjPStr feattype = NULL; ajint sense; float minscore; float maxscore; AjPStr tag = NULL; AjPStr value = NULL; AjBool testscore = AJFALSE; embInit("extractfeat", argc, argv); seqall = ajAcdGetSeqall("sequence"); seqout = ajAcdGetSeqout("outseq"); before = ajAcdGetInt("before"); after = ajAcdGetInt("after"); join = ajAcdGetBoolean("join"); featinname = ajAcdGetBoolean("featinname"); describe = ajAcdGetString("describe"); /* feature filter criteria */ source = ajAcdGetString("source"); feattype = ajAcdGetString("type"); sense = ajAcdGetInt("sense"); minscore = ajAcdGetFloat("minscore"); maxscore = ajAcdGetFloat("maxscore"); tag = ajAcdGetString("tag"); value = ajAcdGetString("value"); testscore = (minscore || maxscore); if(minscore && !maxscore) if(minscore > maxscore) maxscore = minscore; if(!minscore && maxscore) if(minscore > maxscore) minscore = maxscore; while(ajSeqallNext(seqall, &seq)) { /* get the feature table of the sequence */ featab = ajSeqGetFeatCopy(seq); /* delete features in the table that don't match our criteria */ extractfeat_FeatureFilter(featab, source, feattype, sense, testscore, minscore, maxscore, tag, value); /* extract the features */ extractfeat_FeatSeqExtract(seq, seqout, featab, before, after, join, featinname, describe); ajFeattableDel(&featab); } ajSeqoutClose(seqout); ajSeqoutDel(&seqout); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&describe); ajStrDel(&source); ajStrDel(&feattype); ajStrDel(&tag); ajStrDel(&value); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqout seqout; AjPSeq seq; AjPStr name = NULL; AjPStr desc = NULL; AjPStr temp = NULL; AjBool append; embInit("descseq", argc, argv); seqout = ajAcdGetSeqout("outseq"); seq = ajAcdGetSeq("sequence"); append = ajAcdGetBoolean("append"); name = ajAcdGetString("name"); desc = ajAcdGetString("description"); /* if appending, then do this */ if(append) { /* is there a name? */ if(ajStrGetLen(name)) { ajStrAssignS(&temp, ajSeqGetNameS(seq)); ajStrAppendS(&temp, name); ajSeqAssignNameS(seq, temp); } /* is there a description? */ if(ajStrGetLen(desc)) { ajStrAssignS(&temp, ajSeqGetDescS(seq)); ajStrAppendS(&temp, desc); ajSeqAssignDescS(seq, temp); } /* otherwise, just overwrite the existing values */ } else { /* is there a name? */ if(ajStrGetLen(name)) ajSeqAssignNameS(seq, name); /* is there a description? */ if(ajStrGetLen(desc)) ajSeqAssignDescS(seq, desc); } ajSeqoutWriteSeq(seqout, seq); ajSeqoutClose(seqout); ajSeqDel(&seq); ajSeqoutDel(&seqout); ajStrDel(&name); ajStrDel(&desc); ajStrDel(&temp); embExit(); return 0; }