int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq = NULL; AjPReport outf = NULL; AjPFile inf = NULL; ajint begin; ajint end; AjPList l = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPStr line = NULL; AjPStr name = NULL; AjPStr acc = NULL; AjPStr bf = NULL; AjPStr menu; AjPStr pattern = NULL; AjPStr opattern = NULL; AjPStr pname = NULL; AjPStr key = NULL; AjPStr value = NULL; AjPTable atable = NULL; AjPTable btable = NULL; ajint mismatch; ajint minlength; ajint sum; ajint v; char cp; const char *p; embInit("tfscan", argc, argv); seqall = ajAcdGetSeqall("sequence"); outf = ajAcdGetReport("outfile"); mismatch = ajAcdGetInt("mismatch"); minlength = ajAcdGetInt("minlength"); menu = ajAcdGetListSingle("menu"); pname = ajStrNew(); cp=ajStrGetCharFirst(menu); if(cp=='F') ajStrAssignC(&pname,"tffungi"); else if(cp=='I') ajStrAssignC(&pname,"tfinsect"); else if(cp=='O') ajStrAssignC(&pname,"tfother"); else if(cp=='P') ajStrAssignC(&pname,"tfplant"); else if(cp=='V') ajStrAssignC(&pname,"tfvertebrate"); else if(cp=='C') inf = ajAcdGetDatafile("custom"); if(cp!='C') { inf = ajDatafileNewInNameS(pname); if(!inf) ajFatal("Either EMBOSS_DATA undefined or TFEXTRACT needs running"); } name = ajStrNew(); acc = ajStrNew(); bf = ajStrNewC(""); substr = ajStrNew(); line = ajStrNew(); pattern = ajStrNewC("AA"); opattern = ajStrNew(); while(ajSeqallNext(seqall, &seq)) { begin=ajSeqallGetseqBegin(seqall); end=ajSeqallGetseqEnd(seqall); ajStrAssignC(&name,ajSeqGetNameC(seq)); strand=ajSeqGetSeqCopyS(seq); ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1); ajStrFmtUpper(&substr); l=ajListNew(); atable = ajTablestrNew(1000); btable = ajTablestrNew(1000); sum=0; while(ajReadlineTrim(inf,&line)) { p = ajStrGetPtr(line); if(!*p || *p=='#' || *p=='\n' || *p=='!') continue; ajFmtScanS(line,"%S%S%S",&pname,&pattern,&acc); p += ajStrGetLen(pname); while(*p && *p==' ') ++p; p += ajStrGetLen(pattern); while(*p && *p==' ') ++p; p += ajStrGetLen(acc); while(*p && *p==' ') ++p; ajStrAssignS(&opattern,pattern); ajStrAssignC(&bf,p); /* rest of line */ v = embPatVariablePattern(pattern,substr,pname,l,0, mismatch,begin); if(v) { key = ajStrNewS(pname); value = ajStrNewS(acc); ajTablePut(atable,(void *)key,(void *)value); key = ajStrNewS(pname); value = ajStrNewS(bf); ajTablePut(btable,(void *)key,(void *)value); } sum += v; } if(sum) tfscan_print_hits(&l,sum,outf,atable,seq,minlength, btable); ajFileSeek(inf,0L,0); ajListFree(&l); ajTablestrFree(&atable); ajTablestrFree(&btable); ajStrDel(&strand); } ajStrDel(&line); ajStrDel(&name); ajStrDel(&acc); ajStrDel(&pname); ajStrDel(&opattern); ajStrDel(&bf); ajStrDel(&pattern); ajStrDel(&substr); ajSeqDel(&seq); ajFileClose(&inf); ajReportClose(outf); ajReportDel(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&menu); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeq seq = NULL; AjPReport report = NULL; AjPFeattable feat=NULL; AjPStr sstr = NULL; const AjPStr sname = NULL; AjPStr revcomp = NULL; ajint RStotal; AjPStr enzymes = NULL; /* string for RE selection */ AjPList relist = NULL; ajint begin; ajint end; ajint radj; ajint start; AjBool sshow; AjBool tshow; AjBool allmut; AjPList results1 = NULL; /* for forward strand */ AjPList results2 = NULL; /* for reverse strand */ AjPList shits; AjPList nshits; AjPStr tailstr = NULL; embInit("silent", argc, argv); seq = ajAcdGetSeq("sequence"); enzymes = ajAcdGetString("enzymes"); sshow = ajAcdGetBoolean("sshow"); tshow = ajAcdGetBoolean("tshow"); allmut = ajAcdGetBoolean("allmut"); report = ajAcdGetReport ("outfile"); shits = ajListNew(); nshits = ajListNew(); /*calling function to read in RE info*/ RStotal = silent_restr_read(&relist,enzymes); begin = ajSeqGetBegin(seq); /* returns the seq start posn, or 1 if no start has been set */ end = ajSeqGetEnd(seq); /* returns the seq end posn, or seq length if no end has been set */ radj=begin+end+1; /* posn adjustment for complementary strand */ ajStrAssignSubC(&sstr,ajSeqGetSeqC(seq),--begin,--end); ajStrFmtUpper(&sstr); sname = ajSeqGetNameS(seq); ajStrAssignC(&revcomp,ajStrGetPtr(sstr)); ajSeqstrReverse(&revcomp); start = begin+1; feat = ajFeattableNewDna(ajSeqGetNameS(seq)); if(sshow) { silent_fmt_sequence("SEQUENCE", sstr,&tailstr,start,ajTrue); } results1 = silent_mismatch(sstr,relist,&tailstr,sname,RStotal,begin,radj, ajFalse,end,tshow); silent_split_hits(&results1,&shits,&nshits,allmut); ajReportSetHeaderC(report, "KEY:\n" "EnzymeName: Enzyme name\n" "RS-Pattern: Restriction enzyme recognition site " "pattern\n" "Base-Posn: Position of base to be mutated\n" "AAs: Amino acid. Original sequence(.)After mutation\n" "Silent: Yes for unchanged amino acid\n" "Mutation: The base mutation to perform\n\n" "Creating silent and non-silent mutations\n"); silent_fmt_hits(shits,feat, ajTrue, ajFalse); if(allmut) { silent_fmt_hits(nshits,feat, ajFalse, ajFalse); } if(sshow) { silent_fmt_sequence("REVERSE SEQUENCE", revcomp,&tailstr,start,ajTrue); } results2 = silent_mismatch(revcomp,relist,&tailstr, sname,RStotal,begin,radj, ajTrue,end,tshow); silent_split_hits(&results2,&shits,&nshits,allmut); silent_fmt_hits(shits,feat, ajTrue, ajTrue); if(allmut) { silent_fmt_hits(nshits,feat, ajFalse, ajTrue); } ajReportSetStatistics(report, 1, ajSeqGetLenTrimmed(seq)); ajReportSetTailS(report, tailstr); (void) ajReportWrite (report,feat,seq); ajFeattableDel(&feat); ajStrDel(&revcomp); ajStrDel(&enzymes); ajListFree(&results1); ajListFree(&results2); ajListFree(&shits); ajListFree(&nshits); ajReportClose(report); ajReportDel(&report); ajSeqDel(&seq); ajStrDel(&sstr); silent_relistdel(&relist); ajStrDel(&tailstr); embExit(); return 0; }