int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq; AjPFile outf; AjPCod codon; AjPStr substr; ajint beg; ajint end; ajint ccnt; embInit("cusp", argc, argv); seqall = ajAcdGetSeqall("sequence"); outf = ajAcdGetOutfile("outfile"); ccnt = 0; substr = ajStrNew(); codon = ajCodNewCodenum(0); ajCodSetNameS(codon, ajFileGetPrintnameS(outf)); while(ajSeqallNext(seqall, &seq)) { beg = ajSeqallGetseqBegin(seqall); end = ajSeqallGetseqEnd(seqall); ajStrAssignSubS(&substr,ajSeqGetSeqS(seq),beg-1,end-1); ajCodSetTripletsS(codon,substr,&ccnt); } ajCodCalcUsage(codon,ccnt); ajCodSetDescC(codon, "CUSP codon usage file"); ajCodWrite(codon, outf); ajFileClose(&outf); ajStrDel(&substr); ajCodDel(&codon); ajSeqallDel(&seqall); ajSeqDel(&seq); embExit(); return 0; }
int main(int argc, char **argv) { AjPSeqall seqall; AjPSeq seq; AjPFile outf; AjPCod codon; AjPStr substr; AjBool sum; ajint ccnt; ajint beg; ajint end; float Nc; double td; embInit("chips", argc, argv); seqall = ajAcdGetSeqall("seqall"); outf = ajAcdGetOutfile("outfile"); sum = ajAcdGetBoolean("sum"); codon = ajCodNewCodenum(0); ccnt = 0; substr = ajStrNew(); while(ajSeqallNext(seqall, &seq)) { beg = ajSeqallGetseqBegin(seqall); end = ajSeqallGetseqEnd(seqall); ajStrAssignSubS(&substr,ajSeqGetSeqS(seq),beg-1,end-1); ajStrFmtUpper(&substr); ajCodSetTripletsS(codon,substr,&ccnt); if(!sum) { ajCodCalcUsage(codon,ccnt); td = ajCodCalcNc(codon); Nc = (float) td; ajFmtPrintF(outf,"%-20s Nc = %.3f\n",ajSeqGetNameC(seq),Nc); ajCodClearData(codon); } } if(sum) { ajCodCalcUsage(codon,ccnt); td = ajCodCalcNc(codon); Nc = (float) td; ajFmtPrintF(outf,"# CHIPS codon usage statistics\n\n"); ajFmtPrintF(outf,"Nc = %.3f\n",Nc); } ajFileClose(&outf); ajCodDel(&codon); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&substr); embExit(); return 0; }
int main(int argc, char **argv) { const char *codons[]= { "TAG","TAA","TGA","GCG","GCA","GCT","GCC","TGT", /* 00-07 */ "TGC","GAT","GAC","GAA","GAG","TTT","TTC","GGT", /* 08-15 */ "GGG","GGA","GGC","CAT","CAC","ATA","ATT","ATC", /* 16-23 */ "AAA","AAG","CTA","TTA","TTG","CTT","CTC","CTG", /* 24-31 */ "ATG","AAT","AAC","CCG","CCA","CCT","CCC","CAA", /* 32-39 */ "CAG","CGT","CGA","CGC","AGG","AGA","CGG","TCG", /* 40-47 */ "TCA","AGT","TCT","TCC","AGC","ACG","ACT","ACA", /* 48-55 */ "ACC","GTA","GTT","GTC","GTG","TGG","TAT","TAC" /* 56-63 */ }; const char *aa= "***AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY"; AjPFile inf = NULL; AjPFile outf = NULL; char *entryname = NULL; AjPStr fname = NULL; AjPStr key = NULL; AjPStr tmpkey = NULL; AjBool allrecords = AJFALSE; AjPTable table = NULL; ajint i = 0; ajint j = 0; ajint k = 0; ajint x = 0; ajint savecount[3]; AjPStr *keyarray = NULL; CutgPValues *valarray = NULL; AjPCod codon = NULL; ajint sum = 0; char c; AjPList flist = NULL; AjPFile logf = NULL; AjPStr entry = NULL; AjPStr baseentry = NULL; AjPStr wild = NULL; AjPStr division = NULL; AjPStr release = NULL; AjPStr wildspecies = NULL; CutgPValues value = NULL; AjPStr docstr = NULL; AjPStr species = NULL; AjPStr filename = NULL; ajint nstops; embInit("cutgextract",argc,argv); tmpkey = ajStrNew(); fname = ajStrNew(); table = ajTablestrNewLen(TABLE_ESTIMATE); flist = ajAcdGetDirlist("directory"); wild = ajAcdGetString("wildspec"); release = ajAcdGetString("release"); logf = ajAcdGetOutfile("outfile"); wildspecies = ajAcdGetString("species"); filename = ajAcdGetString("filename"); allrecords = ajAcdGetBoolean("allrecords"); ajStrInsertC(&release, 0, "CUTG"); ajStrRemoveWhite(&release); while(ajListPop(flist,(void **)&entry)) { ajStrAssignS(&baseentry, entry); ajFilenameTrimPath(&baseentry); ajDebug("Testing file '%S'\n", entry); if(!ajStrMatchWildS(baseentry,wild)) { ajStrDel(&entry); continue; } ajDebug("... matched wildcard '%S'\n", wild); inf = ajFileNewInNameS(entry); if(!inf) ajFatal("cannot open file %S",entry); ajFmtPrintS(&division, "%F", inf); ajFilenameTrimAll(&division); while((entryname = cutgextract_next(inf, wildspecies, &species, &docstr))) { if(ajStrGetLen(filename)) ajStrAssignS(&tmpkey,filename); else ajStrAssignC(&tmpkey,entryname); /* See if organism is already in the table */ value = ajTableFetch(table,tmpkey); if(!value) /* Initialise */ { key = ajStrNewS(tmpkey); AJNEW0(value); ajStrAssignS(&value->Species,species); ajStrAssignS(&value->Division, division); ajTablePut(table,(void *)key,(void *)value); } for(k=0;k<3;k++) savecount[k] = value->Count[k]; nstops = cutgextract_readcodons(inf,allrecords, value->Count); if(nstops < 1) { value->Skip++; continue; } value->CdsCount++; if(nstops>1) { value->CdsCount += (nstops - 1); value->Warn++; ajWarn("Found %d stop codons (%d %d %d) for CDS '%S'", nstops, value->Count[0] - savecount[0], value->Count[1] - savecount[1], value->Count[2] - savecount[2], cutgextractSavepid); } } ajStrDel(&entry); ajFileClose(&inf); } ajTableToarrayKeysValues(table,(void***) &keyarray, (void***) &valarray); i = 0; while(keyarray[i]) { key = keyarray[i]; value = (CutgPValues) valarray[i++]; codon = ajCodNew(); sum = 0; for(j=0;j<CODONS;++j) { sum += value->Count[j]; x = ajCodIndexC(codons[j]); codon->num[x] = value->Count[j]; c = aa[j]; if(c=='*') codon->aa[x] = 27; else codon->aa[x] = c-'A'; } ajCodCalcUsage(codon,sum); ajStrAppendC(&key, ".cut"); if(allrecords) { if(value->Warn) ajFmtPrintF(logf, "Writing %S CDS: %d Warnings: %d\n", key, value->CdsCount, value->Warn); else ajFmtPrintF(logf, "Writing %S CDS: %d\n", key, value->CdsCount); } else { if(value->Skip) ajFmtPrintF(logf, "Writing %S CDS: %d Skipped: %d\n", key, value->CdsCount, value->Skip); else ajFmtPrintF(logf, "Writing %S CDS: %d\n", key, value->CdsCount); } ajFmtPrintS(&fname,"CODONS/%S",key); outf = ajDatafileNewOutNameS(fname); if(!outf) ajFatal("Cannot open output file %S",fname); ajCodSetNameS(codon, key); ajCodSetSpeciesS(codon, value->Species); ajCodSetDivisionS(codon, value->Division); ajCodSetReleaseS(codon, release); ajCodSetNumcds(codon, value->CdsCount); ajCodSetNumcodons(codon, sum); ajCodWrite(codon, outf); ajFileClose(&outf); ajStrDel(&key); ajStrDel(&value->Division); ajStrDel(&value->Doc); ajStrDel(&value->Species); AJFREE(value); ajCodDel(&codon); } AJFREE(keyarray); AJFREE(valarray); ajTableFree(&table); ajListFree(&flist); ajStrDel(&wild); ajStrDel(&release); ajStrDel(&wildspecies); ajStrDel(&filename); ajFileClose(&logf); ajStrDel(&cutgextractSavepid); ajStrDel(&cutgextractLine); ajStrDel(&cutgextractOrg); ajStrDel(&fname); ajStrDel(&tmpkey); ajStrDel(&species); ajStrDel(&docstr); ajStrDel(&division); ajStrDel(&baseentry); embExit(); return 0; }