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;
}
int main(int argc, char **argv)
{
AjPFile infdat = NULL;
AjPFile infdoc = NULL;
AjPFile outf = NULL;
AjPFile outs = NULL;
AjBool haspattern;
const char *p;
AjPStr line = NULL;
AjPStr text = NULL;
AjPStr dirname = NULL;
AjPStr filename = NULL;
AjPStr id = NULL;
AjPStr ac = NULL;
AjPStr de = NULL;
AjPStr pa = NULL;
AjPStr ps = NULL;
AjPStr fn = NULL;
AjPStr re = NULL;
AjPStr fname = NULL;
AjBool flag;
AjBool isopen;
AjBool goback;
ajlong storepos = 0L;
embInit("prosextract", argc, argv);
dirname = ajAcdGetDirectoryName("prositedir");
line = ajStrNew();
text = ajStrNew();
id = ajStrNew();
ac = ajStrNew();
de = ajStrNew();
pa = ajStrNew();
ps = ajStrNew();
fn=ajStrNew();
ajStrAssignS(&fn,dirname);
ajStrAppendC(&fn,"prosite.dat");
if(!(infdat=ajFileNewInNameS(fn)))
ajFatal("Cannot open file %S",fn);
ajStrDel(&fn);
fn=ajStrNewC("PROSITE/prosite.lines");
outf = ajDatafileNewOutNameS(fn);
ajStrDel(&fn);
haspattern = ajFalse;
while(ajReadlineTrim(infdat, &line) )
{
if(ajStrPrefixC(line, "ID"))
{
if(ajStrSuffixC(line,"PATTERN."))
{
haspattern = ajTrue;
/*save id*/
p = ajStrGetPtr(line);
p = ajSysFuncStrtok(p," \t;");
p = ajSysFuncStrtok(NULL," \t;");
ajStrAssignC(&id,p);
ajFmtPrintF(outf, "%S ", id);
continue;
}
else
{
haspattern = ajFalse;
continue;
}
}
if(!haspattern)
continue;
if(ajStrPrefixC(line, "AC") )
{
p = ajStrGetPtr(line);
p = ajSysFuncStrtok(p, " \t;");
p = ajSysFuncStrtok(NULL, " \t;");
ajStrAssignC(&ac,p);
ajFmtPrintF(outf, "%S\n ", ac);
continue;
}
if(ajStrPrefixC(line, "DE") )
{
p = ajStrGetPtr(line);
p = ajSysFuncStrtok(p, " \t.");
p = ajSysFuncStrtok(NULL, " \t.");
ajStrAssignC(&de,p);
ajFmtPrintF(outf, "%S\n ", de);
continue;
}
if(ajStrPrefixC(line, "PA"))
{
ajStrAssignC(&pa,"");
while(ajStrPrefixC(line,"PA"))
{
p = ajStrGetPtr(line);
p = ajSysFuncStrtok(p, " \t.");
p = ajSysFuncStrtok(NULL, " \t.");
ajStrAppendC(&pa,p);
ajReadlineTrim(infdat, &line);
}
ajFmtPrintF(outf, "%S\n", pa);
re = embPatPrositeToRegExp(pa);
ajFmtPrintF(outf, "^%S\n\n", re);
ajStrDel(&re);
continue;
}
}
/* Finished processing prosite.dat so look at prosite.doc */
fn = ajStrNew();
ajStrAssignS(&fn,dirname);
ajStrAppendC(&fn,"prosite.doc");
if(!(infdoc=ajFileNewInNameS(fn)))
ajFatal("Cannot open file %S",fn);
ajStrDel(&fn);
fname = ajStrNewC("PROSITE/");
flag = ajFalse;
isopen = ajFalse;
goback = ajFalse;
while(ajReadlineTrim(infdoc, &text))
{
if(ajStrPrefixC(text, "{PS") && isopen && !goback)
goback = ajTrue;
if(ajStrPrefixC(text, "{PS") && !isopen)
{
storepos = ajFileResetPos(infdoc);
/* save out the documentation text to acc numbered outfiles . */
p = ajStrGetPtr(text)+1;
p = ajSysFuncStrtok(p, ";");
ajStrAssignS(&filename, fname);
ajStrAppendC(&filename, p);
outs = ajDatafileNewOutNameS(filename);
flag = ajTrue;
isopen = ajTrue;
continue;
}
if(ajStrPrefixC(text, "{BEGIN}") && flag)
{
while(ajReadlineTrim(infdoc, &text))
{
if(ajStrPrefixC(text,"{END}"))
break;
ajFmtPrintF(outs, "%S\n", text);
}
ajFileClose(&outs);
isopen = ajFalse;
if(goback)
{
goback = ajFalse;
ajFileSeek(infdoc,storepos,0);
}
}
}
ajStrDel(&line);
ajStrDel(&text);
ajStrDel(&dirname);
ajStrDel(&filename);
ajStrDel(&id);
ajStrDel(&ac);
ajStrDel(&de);
ajStrDel(&pa);
ajStrDel(&re);
ajStrDel(&ps);
ajStrDel(&fname);
ajFileClose(&infdat);
ajFileClose(&infdoc);
ajFileClose(&outf);
embExit();
return 0;
}
