static AjBool dbxflat_ParseEmbl(EmbPBtreeEntry entry, AjPFile inf)
{
AjPStr line = NULL;
ajlong pos = 0L;
line = ajStrNewC("");
while(!ajStrPrefixC(line,"//"))
{
pos = ajFileResetPos(inf);
if(!ajReadlineTrim(inf,&line))
{
ajStrDel(&line);
return ajFalse;
}
if(ajStrPrefixC(line,"ID"))
{
entry->fpos = pos;
ajFmtScanS(line,"%*S%S",&entry->id);
ajStrTrimEndC(&entry->id, ";");
/*
++global;
printf("%d. %s\n",global,ajStrGetPtr(entry->id));
*/
if(svfield)
embBtreeEmblSV(line,svfield->data);
}
if(svfield)
if(ajStrPrefixC(line,"SV") ||
ajStrPrefixC(line,"IV")) /* emblcds database format */
embBtreeEmblAC(line,svfield->data);
if(accfield)
if(ajStrPrefixC(line,"AC") ||
ajStrPrefixC(line,"PA")) /* emblcds database format */
embBtreeEmblAC(line,accfield->data);
if(keyfield)
if(ajStrPrefixC(line,"KW"))
embBtreeEmblKW(line,keyfield->data,keyfield->len);
if(desfield)
if(ajStrPrefixC(line,"DE"))
embBtreeEmblDE(line,desfield->data,desfield->len);
if(orgfield)
if(ajStrPrefixC(line,"OC") || ajStrPrefixC(line,"OS"))
embBtreeEmblTX(line,orgfield->data,orgfield->len);
}
ajStrDel(&line);
return ajTrue;
}
static AjBool dbxflat_ParseEmbl(EmbPBtreeEntry entry, AjPFile inf)
{
AjPStr line = NULL;
ajlong pos = 0L;
line = ajStrNewC("");
while(!ajStrPrefixC(line,"//"))
{
pos = ajFileResetPos(inf);
if(!ajReadlineTrim(inf,&line))
{
ajStrDel(&line);
return ajFalse;
}
if(ajStrPrefixC(line,"ID"))
{
entry->fpos = pos;
ajFmtScanS(line,"%*S%S",&entry->id);
ajStrTrimEndC(&entry->id, ";");
/*
++global;
printf("%d. %s\n",global,ajStrGetPtr(entry->id));
*/
if(entry->do_sv)
embBtreeEmblSV(line,entry->sv);
}
if(entry->do_sv)
if(ajStrPrefixC(line,"SV") ||
ajStrPrefixC(line,"IV")) /* emblcds database format */
embBtreeEmblAC(line,entry->sv);
if(entry->do_accession)
if(ajStrPrefixC(line,"AC") ||
ajStrPrefixC(line,"PA")) /* emblcds database format */
embBtreeEmblAC(line,entry->ac);
if(entry->do_keyword)
if(ajStrPrefixC(line,"KW"))
embBtreeEmblKW(line,entry->kw,entry->kwlen);
if(entry->do_description)
if(ajStrPrefixC(line,"DE"))
embBtreeEmblDE(line,entry->de,entry->delen);
if(entry->do_taxonomy)
if(ajStrPrefixC(line,"OC") || ajStrPrefixC(line,"OS"))
embBtreeEmblTX(line,entry->tx,entry->txlen);
}
ajStrDel(&line);
return ajTrue;
}
static AjBool dbifasta_ParseFasta(AjPFile libr, ajint* dpos,
ajint* maxFieldLen, ajuint* countfield,
AjPRegexp idexp,
ajuint usertype, AjPFile* alistfile,
AjBool systemsort, AjPStr const * fields)
{
char* fd;
ajlong ipos;
static AjPStr tstr = NULL;
static ajint numFields;
static ajint accfield = -1;
static ajint desfield = -1;
static ajint svnfield = -1;
static AjBool reset = AJTRUE;
ajuint type = usertype;
if(!fields)
{
reset = ajTrue;
accfield = svnfield = desfield = -1;
return ajFalse;
}
if(reset)
{
numFields = 0;
while(fields[numFields])
{
if(ajStrMatchCaseC(fields[numFields], "acc"))
accfield=numFields;
else if(ajStrMatchCaseC(fields[numFields], "sv"))
svnfield=numFields;
else if(ajStrMatchCaseC(fields[numFields], "des"))
desfield=numFields;
else
ajWarn("EMBL parsing unknown field '%S' ignored",
fields[numFields]);
numFields++;
}
reset = ajFalse;
}
if(!dbifastaGWrdexp)
dbifastaGWrdexp = ajRegCompC("([A-Za-z0-9]+)");
if(!tstr)
tstr = ajStrNew();
*dpos = (ajint) ajFileResetPos(libr); /* Lossy cast */
ajReadline(libr, &dbifastaGRline);
if(!ajStrGetLen(dbifastaGRline))
return ajFalse;
if(!ajRegExec(idexp,dbifastaGRline))
{
ajStrDelStatic(&dbifastaGTmpAc);
type = FASTATYPE_SIMPLE;
idexp = dbifastaGIdexp;
if(!ajRegExec(idexp, dbifastaGRline))
{
ajFatal("Unrecognised ID line format: %S", dbifastaGRline);
return ajFalse;
}
ajWarn("Invalid ID line for selected format: %S", dbifastaGRline);
}
/*
** each case needs to set id, tmpac, tmpsv, tmpdes
** using empty values if they are not found
*/
ajStrAssignC(&dbifastaGTmpSv, "");
ajStrAssignC(&dbifastaGTmpGi, "");
ajStrAssignC(&dbifastaGTmpDb, "");
ajStrAssignC(&dbifastaGTmpDes, "");
ajStrAssignC(&dbifastaGTmpAc, "");
ajStrAssignC(&dbifastaGTmpId, "");
switch(type)
{
case FASTATYPE_SIMPLE:
ajRegSubI(idexp,2,&dbifastaGTmpId);
ajStrAssignS(&dbifastaGTmpAc,dbifastaGTmpId);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
case FASTATYPE_DBID:
ajRegSubI(idexp,1,&dbifastaGTmpId);
ajStrAssignS(&dbifastaGTmpAc,dbifastaGTmpId);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
case FASTATYPE_GCGID:
ajRegSubI(idexp,1,&dbifastaGTmpId);
ajStrAssignS(&dbifastaGTmpAc,dbifastaGTmpId);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
case FASTATYPE_NCBI:
if(!ajSeqParseNcbi(dbifastaGRline, &dbifastaGTmpId, &dbifastaGTmpAc,
&dbifastaGTmpSv, &dbifastaGTmpGi, &dbifastaGTmpDb,
&dbifastaGTmpDes))
{
ajStrDelStatic(&dbifastaGTmpAc);
return ajFalse;
}
break;
case FASTATYPE_GCGIDACC:
ajRegSubI(idexp,1,&dbifastaGTmpId);
ajRegSubI(idexp,2,&dbifastaGTmpAc);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
case FASTATYPE_GCGACCID:
ajRegSubI(idexp,1,&dbifastaGTmpAc);
ajRegSubI(idexp,2,&dbifastaGTmpId);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
case FASTATYPE_IDACC:
ajRegSubI(idexp,1,&dbifastaGTmpId);
ajRegSubI(idexp,2,&dbifastaGTmpAc);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
case FASTATYPE_ACCID:
ajRegSubI(idexp,1,&dbifastaGTmpAc);
ajRegSubI(idexp,2,&dbifastaGTmpId);
ajRegPost(idexp, &dbifastaGTmpDes);
break;
default:
ajStrDelStatic(&dbifastaGTmpAc);
return ajFalse;
}
ajStrFmtUpper(&dbifastaGTmpId);
ajStrFmtUpper(&dbifastaGTmpAc);
if(accfield >= 0)
embDbiMaxlen(&dbifastaGTmpAc, &maxFieldLen[accfield]);
if(svnfield >= 0)
{
embDbiMaxlen(&dbifastaGTmpSv, &maxFieldLen[svnfield]);
embDbiMaxlen(&dbifastaGTmpGi, &maxFieldLen[svnfield]);
}
if(systemsort)
{
if(accfield >= 0 && ajStrGetLen(dbifastaGTmpAc))
{
countfield[accfield]++;
ajFmtPrintF(alistfile[accfield], "%S %S\n",
dbifastaGTmpId, dbifastaGTmpAc);
}
if(svnfield >= 0 && ajStrGetLen(dbifastaGTmpSv))
{
countfield[svnfield]++;
ajFmtPrintF(alistfile[svnfield], "%S %S\n",
dbifastaGTmpId, dbifastaGTmpSv);
}
if(svnfield >= 0 && ajStrGetLen(dbifastaGTmpGi))
{
countfield[svnfield]++;
ajFmtPrintF(alistfile[svnfield], "%S %S\n",
dbifastaGTmpId, dbifastaGTmpGi);
}
if(desfield >= 0 && ajStrGetLen(dbifastaGTmpDes))
while(ajRegExec(dbifastaGWrdexp, dbifastaGTmpDes))
{
ajRegSubI(dbifastaGWrdexp, 1, &dbifastaGTmpFd);
embDbiMaxlen(&dbifastaGTmpFd, &maxFieldLen[desfield]);
ajStrFmtUpper(&dbifastaGTmpFd);
ajDebug("++des '%S' tmpdes '%S\n",
dbifastaGTmpFd, dbifastaGTmpDes);
countfield[desfield]++;
ajFmtPrintF(alistfile[desfield], "%S %S\n",
dbifastaGTmpId, dbifastaGTmpFd);
ajRegPost(dbifastaGWrdexp, &dbifastaGTmpDes);
}
}
else
{
if(accfield >= 0 && ajStrGetLen(dbifastaGTmpAc))
{
fd = ajCharNewS(dbifastaGTmpAc);
ajListPushAppend(dbifastaGFdl[accfield],fd);
countfield[accfield]++;
}
if(svnfield >= 0 && ajStrGetLen(dbifastaGTmpSv))
{
fd = ajCharNewS(dbifastaGTmpSv);
ajListPushAppend(dbifastaGFdl[svnfield], fd);
countfield[svnfield]++;
}
if(svnfield >= 0 && ajStrGetLen(dbifastaGTmpGi))
{
fd = ajCharNewS(dbifastaGTmpGi);
ajListPushAppend(dbifastaGFdl[svnfield], fd);
countfield[svnfield]++;
}
if(desfield >= 0 && ajStrGetLen(dbifastaGTmpDes))
while(ajRegExec(dbifastaGWrdexp, dbifastaGTmpDes))
{
ajRegSubI(dbifastaGWrdexp, 1, &dbifastaGTmpFd);
embDbiMaxlen(&dbifastaGTmpFd, &maxFieldLen[desfield]);
ajStrFmtUpper(&dbifastaGTmpFd);
ajDebug("++des '%S' tmpdes: '%S'\n",
dbifastaGTmpFd, dbifastaGTmpDes);
fd = ajCharNewS(dbifastaGTmpFd);
ajListPushAppend(dbifastaGFdl[desfield], fd);
countfield[desfield]++;
ajRegPost(dbifastaGWrdexp, &dbifastaGTmpDes);
}
}
ipos = ajFileResetPos(libr);
while(ajReadline(libr, &dbifastaGRline))
{
if(ajStrGetCharFirst(dbifastaGRline) == '>')
{
ajFileSeek(libr, ipos, 0);
return ajTrue;
}
ipos = ajFileResetPos(libr);
}
ajFileSeek(libr, ipos, 0); /* end of file reached */
return ajTrue;
}
static AjBool dbxflat_ParseFastq(EmbPBtreeEntry entry, AjPFile inf)
{
AjPStr line = NULL;
ajlong pos = 0L;
ajuint seqlen = 0;
ajuint qlen = 0;
AjPStr tmpfd = NULL;
AjPStr str = NULL;
AjPStr de = NULL;
AjBool ok;
if(!dbxflat_wrdexp)
dbxflat_wrdexp = ajRegCompC("([A-Za-z0-9.:=]+)");
line = ajStrNewC("");
pos = ajFileResetPos(inf);
if(!ajReadlineTrim(inf,&line))
{
ajStrDel(&line);
return ajFalse;
}
/* first line of entry */
if(!ajStrPrefixC(line,"@"))
return ajFalse;
entry->fpos = pos;
ajStrCutStart(&line, 1);
ajStrExtractFirst(line, &de, &entry->id);
if(desfield && ajStrGetLen(de))
{
while(ajRegExec(dbxflat_wrdexp,de))
{
ajRegSubI(dbxflat_wrdexp, 1, &tmpfd);
str = ajStrNew();
ajStrAssignS(&str,tmpfd);
ajListPush(desfield->data,(void *)str);
ajRegPost(dbxflat_wrdexp, &de);
}
}
/* now read sequence */
ok = ajReadlineTrim(inf,&line);
while(ok && !ajStrPrefixC(line, "+"))
{
ajStrRemoveWhite(&line);
seqlen += MAJSTRGETLEN(line);
ok = ajReadlineTrim(inf,&line);
}
if(!ok)
return ajFalse;
ok = ajReadlineTrim(inf,&line);
while(ok)
{
qlen += MAJSTRGETLEN(line);
if(qlen < seqlen)
ok = ajReadlineTrim(inf,&line);
else
ok = ajFalse;
}
ajStrDel(&de);
ajStrDel(&tmpfd);
ajStrDel(&line);
return ajTrue;
}
static AjBool dbxflat_ParseGenbank(EmbPBtreeEntry entry, AjPFile inf)
{
AjPStr line = NULL;
ajlong pos = 0L;
AjBool ret = ajTrue;
AjPStr sumline = NULL;
line = ajStrNewC("");
sumline = ajStrNew();
while(!ajStrPrefixC(line,"//") && ret)
{
if(ajStrPrefixC(line,"LOCUS"))
{
entry->fpos = pos;
ajFmtScanS(line,"%*S%S",&entry->id);
}
if(svfield)
if(ajStrPrefixC(line,"VERSION"))
embBtreeGenBankAC(line,svfield->data);
if(accfield)
if(ajStrPrefixC(line,"ACCESSION"))
embBtreeGenBankAC(line,accfield->data);
if(keyfield)
if(ajStrPrefixC(line,"KEYWORDS"))
{
ajStrAssignS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
while(ret && *MAJSTRGETPTR(line)==' ')
{
ajStrAppendS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
}
ajStrRemoveWhiteExcess(&sumline);
embBtreeGenBankKW(sumline,keyfield->data,keyfield->len);
continue;
}
if(desfield)
if(ajStrPrefixC(line,"DEFINITION"))
{
ajStrAssignS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
while(ret && *MAJSTRGETPTR(line)==' ')
{
ajStrAppendS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
}
ajStrRemoveWhiteExcess(&sumline);
embBtreeGenBankDE(sumline,desfield->data,desfield->len);
continue;
}
if(orgfield)
if(ajStrPrefixC(line,"SOURCE"))
{
ret = ajReadlineTrim(inf,&line);
ajStrAppendC(&line,";");
while(ret && *MAJSTRGETPTR(line)==' ')
{
ajStrAppendS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
}
ajStrRemoveWhiteExcess(&sumline);
embBtreeGenBankTX(sumline,orgfield->data,orgfield->len);
continue;
}
pos = ajFileResetPos(inf);
if(!ajReadlineTrim(inf,&line))
ret = ajFalse;
}
ajStrDel(&line);
ajStrDel(&sumline);
return ret;
}
static AjBool dbxflat_ParseGenbank(EmbPBtreeEntry entry, AjPFile inf)
{
AjPStr line = NULL;
ajlong pos = 0L;
AjBool ret = ajTrue;
AjPStr sumline = NULL;
line = ajStrNewC("");
sumline = ajStrNew();
while(!ajStrPrefixC(line,"//") && ret)
{
if(ajStrPrefixC(line,"LOCUS"))
{
entry->fpos = pos;
ajFmtScanS(line,"%*S%S",&entry->id);
}
if(entry->do_sv)
if(ajStrPrefixC(line,"VERSION"))
embBtreeGenBankAC(line,entry->sv);
if(entry->do_accession)
if(ajStrPrefixC(line,"ACCESSION"))
embBtreeGenBankAC(line,entry->ac);
if(entry->do_keyword)
if(ajStrPrefixC(line,"KEYWORDS"))
{
ajStrAssignS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
while(ret && *MAJSTRGETPTR(line)==' ')
{
ajStrAppendS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
}
ajStrRemoveWhiteExcess(&sumline);
embBtreeGenBankKW(sumline,entry->kw,entry->kwlen);
continue;
}
if(entry->do_description)
if(ajStrPrefixC(line,"DEFINITION"))
{
ajStrAssignS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
while(ret && *MAJSTRGETPTR(line)==' ')
{
ajStrAppendS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
}
ajStrRemoveWhiteExcess(&sumline);
embBtreeGenBankDE(sumline,entry->de,entry->delen);
continue;
}
if(entry->do_taxonomy)
if(ajStrPrefixC(line,"SOURCE"))
{
ret = ajReadlineTrim(inf,&line);
ajStrAppendC(&line,";");
while(ret && *MAJSTRGETPTR(line)==' ')
{
ajStrAppendS(&sumline,line);
ret = ajReadlineTrim(inf,&line);
}
ajStrRemoveWhiteExcess(&sumline);
embBtreeGenBankTX(sumline,entry->tx,entry->txlen);
continue;
}
pos = ajFileResetPos(inf);
if(!ajReadlineTrim(inf,&line))
ret = ajFalse;
}
ajStrDel(&line);
ajStrDel(&sumline);
return ret;
}
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;
}
