static AjBool dbiblast_wrongtype(const AjPStr oname, const char *suff)
{
ajint itype;
for(itype=0; blasttypes[itype].ExtT; itype++)
{
if(strcmp(suff, blasttypes[itype].ExtT))
if(ajStrSuffixC(oname, blasttypes[itype].ExtT))
return ajTrue;
if(strcmp(suff, blasttypes[itype].ExtH))
if(ajStrSuffixC(oname, blasttypes[itype].ExtH))
return ajTrue;
if(strcmp(suff, blasttypes[itype].ExtS))
if(ajStrSuffixC(oname, blasttypes[itype].ExtS))
return ajTrue;
}
return ajFalse;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPFile primfile;
AjPStr rdline = NULL;
Primer primdata;
AjPStrTok handle = NULL;
AjPList primList = NULL;
embInit("stssearch", argc, argv);
primfile = ajAcdGetInfile("infile");
out = ajAcdGetOutfile("outfile");
seqall = ajAcdGetSeqall("seqall");
while(ajReadlineTrim(primfile, &rdline))
{
if(ajStrGetCharFirst(rdline) == '#')
continue;
if(ajStrSuffixC(rdline, ".."))
continue;
AJNEW(primdata);
primdata->Name = NULL;
primdata->Oligoa = NULL;
primdata->Oligob = NULL;
handle = ajStrTokenNewC(rdline, " \t");
ajStrTokenNextParse(&handle, &primdata->Name);
if(!(nprimers % 1000))
ajDebug("Name [%d]: '%S'\n", nprimers, primdata->Name);
ajStrTokenNextParse(&handle, &primdata->Oligoa);
ajStrFmtUpper(&primdata->Oligoa);
primdata->Prima = ajRegComp(primdata->Oligoa);
ajStrTokenNextParse(&handle, &primdata->Oligob);
ajStrFmtUpper(&primdata->Oligob);
primdata->Primb = ajRegComp(primdata->Oligob);
ajStrTokenDel(&handle);
if(!nprimers)
primList = ajListNew();
ajListPushAppend(primList, primdata);
nprimers++;
}
if(!nprimers)
ajFatal("No primers read\n");
ajDebug("%d primers read\n", nprimers);
while(ajSeqallNext(seqall, &seq))
{
ajSeqFmtUpper(seq);
ajStrAssignS(&seqstr, ajSeqGetSeqS(seq));
ajStrAssignS(&revstr, ajSeqGetSeqS(seq));
ajSeqstrReverse(&revstr);
ajDebug("Testing: %s\n", ajSeqGetNameC(seq));
ntests = 0;
ajListMap(primList, stssearch_primTest, NULL);
}
ajFileClose(&out);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajFileClose(&out);
ajStrDel(&revstr);
ajStrDel(&seqstr);
ajFileClose(&primfile);
ajListMap(primList, stssearch_primDel, NULL);
ajListFree(&primList);
ajStrDel(&rdline);
embExit();
return 0;
}
static void primersearch_read_primers(AjPList *primerList, AjPFile primerFile,
ajint mmp)
{
AjPStr rdline = NULL;
AjPStrTok handle = NULL;
ajint nprimers = 0;
Primer primdata = NULL;
while (ajReadlineTrim(primerFile, &rdline))
{
primdata = NULL;
if (ajStrGetCharFirst(rdline) == '#')
continue;
if (ajStrSuffixC(rdline, ".."))
continue;
AJNEW(primdata);
primdata->Name = NULL;
primersearch_initialise_pguts(&primdata->forward);
primersearch_initialise_pguts(&primdata->reverse);
primdata->hitlist = ajListNew();
handle = ajStrTokenNewC(rdline, " \t");
ajStrTokenNextParse(&handle, &primdata->Name);
ajStrTokenNextParse(&handle, &primdata->forward->patstr);
ajStrFmtUpper(&primdata->forward->patstr);
ajStrTokenNextParse(&handle, &primdata->reverse->patstr);
ajStrFmtUpper(&primdata->reverse->patstr);
ajStrTokenDel(&handle);
/* copy patterns for Henry Spencer code */
ajStrAssignC(&primdata->forward->origpat,
ajStrGetPtr(primdata->forward->patstr));
ajStrAssignC(&primdata->reverse->origpat,
ajStrGetPtr(primdata->reverse->patstr));
/* set the mismatch level */
primdata->forward->mm = (ajint)
(ajStrGetLen(primdata->forward->patstr)*mmp)/100;
primdata->reverse->mm = (ajint)
(ajStrGetLen(primdata->reverse->patstr)*mmp)/100;
if(primersearch_classify_and_compile(&primdata))
{
ajListPushAppend(*primerList, primdata);
nprimers++;
}
else /* there was something funny about the primer sequences */
{
ajUser("Cannot use %s\n", ajStrGetPtr(primdata->Name));
primersearch_free_pguts(&primdata->forward);
primersearch_free_pguts(&primdata->reverse);
ajStrDel(&primdata->Name);
ajListFree(&primdata->hitlist);
ajListFree(&primdata->hitlist);
AJFREE(primdata);
}
}
ajStrDel(&rdline);
return;
}
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;
}
