int main(int argc, char **argv)
{
AjPFile key_inf=NULL; /* File pointer for keywords file. */
AjPFile sp_inf =NULL; /* File pointer for swissprot database. */
AjPFile outf =NULL; /* File pointer for output file. */
AjPTerms keyptr =NULL; /* Pointer to terms structure. */
EmbPHitlist hitptr =NULL; /* Pointer to hitlist structure. */
/* Read data from acd */
embInitPV("seqwords",argc,argv,"DOMSEARCH",VERSION);
key_inf = ajAcdGetInfile("keyfile");
sp_inf = ajAcdGetInfile("spfile");
outf = ajAcdGetOutfile("outfile");
/* Start of main application loop. */
/* Read next list of terms from input file. */
while((seqwords_TermsRead(key_inf, &keyptr)))
{
/* Rewind swissprot file pointer to the top. */
ajFileSeek(sp_inf, 0, 0);
/* Allocate memory for hitlist. */
AJNEW0(hitptr);
/* Do search of swissprot. */
seqwords_keysearch(sp_inf, keyptr, &hitptr);
/* Copy scop records from terms to hitlist structure. */
hitptr->Type = keyptr->Type;
ajStrAssignRef(&hitptr->Class, keyptr->Class);
ajStrAssignRef(&hitptr->Architecture, keyptr->Architecture);
ajStrAssignRef(&hitptr->Topology, keyptr->Topology);
ajStrAssignRef(&hitptr->Fold, keyptr->Fold);
ajStrAssignRef(&hitptr->Superfamily, keyptr->Superfamily);
ajStrAssignRef(&hitptr->Family, keyptr->Family);
/* Write output file. */
embHitlistWriteFasta(outf, hitptr);
/* Free memory for hitlist & keyptr*/
embHitlistDel(&hitptr);
seqwords_TermsDel(&keyptr);
}
seqwords_TermsDel(&keyptr);
/* Tidy up*/
ajFileClose(&key_inf);
ajFileClose(&sp_inf);
ajFileClose(&outf);
embExit();
return 0;
}
/* @funcstatic domainalign_keepsinglets ***************************************
**
** Write singlet sequences to file.
**
** @param [r] domain [AjPDomain]
** @param [r] noden [ajint]
** @param [r] singlets [AjPDirout]
** @param [r] logf [AjPFile]
**
** @return [void] True on success
** @@
****************************************************************************/
static void domainalign_keepsinglets(AjPDomain domain,
ajint noden,
AjPDirout singlets,
AjPFile logf)
{
AjPStr temp2 = NULL; /* A temporary string. */
AjPFile singf = NULL; /* File pointer for singlets file. */
EmbPHitlist hitlist = NULL; /* Hitlist object for output of data. */
temp2 = ajStrNew();
domainalign_writesid(domain, noden, &temp2);
if(MAJSTRGETLEN(ajDomainGetSeqPdb(domain)))
{
/* Write Hit object. */
hitlist = embHitlistNew(1);
hitlist->Type = domain->Type;
ajStrAssignS(&hitlist->hits[0]->Seq, ajDomainGetSeqPdb(domain));
ajStrAssignS(&hitlist->hits[0]->Acc, ajDomainGetAcc(domain));
ajStrAssignS(&hitlist->hits[0]->Spr, ajDomainGetSpr(domain));
ajStrAssignS(&hitlist->hits[0]->Dom, ajDomainGetId(domain));
if((domain->Type == ajSCOP))
{
ajStrAssignS(&hitlist->Class, domain->Scop->Class);
ajStrAssignS(&hitlist->Fold, domain->Scop->Fold);
ajStrAssignS(&hitlist->Superfamily, domain->Scop->Superfamily);
ajStrAssignS(&hitlist->Family, domain->Scop->Family);
if(noden==4)
hitlist->Sunid_Family = domain->Scop->Sunid_Family;
else if(noden==3)
hitlist->Sunid_Family = domain->Scop->Sunid_Superfamily;
else if(noden==2)
hitlist->Sunid_Family = domain->Scop->Sunid_Fold;
else if(noden==1)
hitlist->Sunid_Family = domain->Scop->Sunid_Class;
}
else
{
ajStrAssignS(&hitlist->Class, domain->Cath->Class);
ajStrAssignS(&hitlist->Architecture, domain->Cath->Architecture);
ajStrAssignS(&hitlist->Topology, domain->Cath->Topology);
ajStrAssignS(&hitlist->Superfamily, domain->Cath->Superfamily);
if(noden==9)
hitlist->Sunid_Family = domain->Cath->Family_Id;
if(noden==8)
hitlist->Sunid_Family = domain->Cath->Superfamily_Id;
else if(noden==7)
hitlist->Sunid_Family = domain->Cath->Topology_Id;
else if(noden==6)
hitlist->Sunid_Family = domain->Cath->Arch_Id;
else if(noden==5)
hitlist->Sunid_Family = domain->Cath->Class_Id;
}
singf = ajFileNewOutNameDirS(temp2, singlets);
embHitlistWriteFasta(singf, hitlist);
/* ajFmtPrintF(singf, ">%S\n%S\n", temp2, ajDomainGetSeqPdb(domain)); */
ajFileClose(&singf);
}
else
{
ajWarn("No sequence found (no 'DS' record in DCF file) for singlet %S "
"despite configuring to save singlets. "
"NO file written!", ajDomainGetId(domain));
ajFmtPrintF(logf, "No sequence found (no 'DS' record in DCF file) for "
"singlet %S despite configuring to save singlets. "
"NO file written!", ajDomainGetId(domain));
}
ajStrDel(&temp2);
return;
}