/* @prog scopparse ************************************************************
**
** Converts raw scop classification files to a file in embl-like format.
**
******************************************************************************/
int main(int argc, char **argv)
{
AjPFile inf1 = NULL;
AjPFile inf2 = NULL;
AjPFile outf = NULL;
AjPList list = NULL;
AjPScop tmp = NULL;
AjBool nosegments = ajFalse;
AjBool nomultichain = ajFalse;
AjBool nominor = ajFalse;
/* Read data from acd. */
embInitPV("scopparse", argc, argv, "DOMAINATRIX",VERSION);
inf1 = ajAcdGetInfile("classfile");
inf2 = ajAcdGetInfile("desinfile");
outf = ajAcdGetOutfile("dcffile");
nosegments = ajAcdGetBoolean("nosegments");
nomultichain = ajAcdGetBoolean("nomultichain");
nominor = ajAcdGetBoolean("nominor");
/*
ajFmtPrint("nosegments: %B\n", nosegments);
ajFmtPrint("nomultichain: %B\n", nomultichain);
ajFmtPrint("nominor: %B\n", nominor);
*/
/* Main body of code. */
list = ajScopReadAllRawNew(inf1, inf2, nomultichain);
while(ajListPop(list, (void **) &tmp))
{
if(((!nosegments) || (tmp->N == 1)) &&
((!nominor) || ((tmp->Sunid_Class == 46456) || /* All alpha*/
(tmp->Sunid_Class == 48724) || /* All beta */
(tmp->Sunid_Class == 51349) || /* a/b */
(tmp->Sunid_Class == 53931)))) /* a+b */
ajScopWrite(outf, tmp);
ajScopDel(&tmp);
}
/* Memory management. */
ajFileClose(&outf);
ajFileClose(&inf1);
ajFileClose(&inf2);
ajListFree(&list);
ajExit();
return 0;
}
/* @prog ssematch ***********************************************************
**
** Searches a DCF file (domain classification file) for secondary structure
** matches.
**
****************************************************************************/
int main(int argc, char **argv)
{
/* Variables declarations */
AjPFile dcfin = NULL; /* Domain classification file */
AjPFile ssin = NULL; /* Secondary structure input file*/
AjPMatrixf matrix = NULL; /* Substitution matrix */
AjPFile out_ss = NULL; /* For ss top matches*/
AjPFile out_se = NULL; /* For se top matches*/
AjPFile outfile = NULL; /* Output file*/
AjPFile logf = NULL; /* Log file */
float gapopen_sss = 0.0; /* Gap insertion penalty */
float gapopen_sse = 0.0;
float gapopen = 0.0;
float gapextend_sss = 0.0; /* Gap extension penalty */
float gapextend_sse = 0.0;
float gapextend = 0.0;
ajint max_hits = 0; /* number of top alignments to display*/
ajint mode = 0;
ajint x = 0;
AjPScop temp_scop = NULL; /* scop object pointer*/
AjPList scop_list = NULL; /* list of scop objects for entire domain
classification file */
AjIList iter = NULL;
AjPStr msg = NULL; /* Pointer to String used for messages */
AjPStr line = NULL;
AjPStr qse = NULL; /* query secondary structure elements*/
AjPStr qss = NULL; /* query secondary structure (by residue)*/
AjPSeq q3se = NULL; /* query secondary structure elements, 3-letter
code*/
AjPSeq q3ss = NULL; /* query secondary structure
(by residue), 3-letter code*/
AjPSeq query = NULL;
/* Read data from acd */
embInitPV("ssematch",argc,argv,"DOMAINATRIX",VERSION);
dcfin = ajAcdGetInfile("dcfinfile");
ssin = ajAcdGetInfile("ssinfile");
max_hits = ajAcdGetInt("maxhits");
matrix = ajAcdGetMatrixf("datafile");
gapopen_sss = ajAcdGetFloat("rgapopen");
gapextend_sss = ajAcdGetFloat("rgapextend");
gapopen_sse = ajAcdGetFloat("egapopen");
gapextend_sse = ajAcdGetFloat("egapextend");
out_ss = ajAcdGetOutfile("outssfile");
out_se = ajAcdGetOutfile("outsefile");
logf = ajAcdGetOutfile("logfile");
/* Create list of scop objects for entire input domain classification file. */
scop_list = ajListNew();
while((temp_scop = (ajScopReadCNew(dcfin, "*"))))
ajListPushAppend(scop_list,temp_scop);
/* Error handing if domain classification file was empty. */
if(!(ajListGetLength(scop_list)))
{
ajWarn("Empty list from scop input file\n");
ajFileClose(&dcfin);
ajFileClose(&ssin);
ajMatrixfDel(&matrix);
ajFileClose(&out_ss);
ajFileClose(&out_se);
ajFileClose(&logf);
while(ajListPop(scop_list, (void *) &temp_scop))
ajScopDel(&temp_scop);
ajListFree(&scop_list);
ajListIterDel(&iter);
ajExit();
return 1;
}
/* Error handling in case of empty query file. */
if(ssin == NULL)
{
ajWarn("Empty secondary structure query file\n");
ajFileClose(&dcfin);
ajFileClose(&ssin);
ajMatrixfDel(&matrix);
ajFileClose(&out_ss);
ajFileClose(&out_se);
ajFileClose(&logf);
while(ajListPop(scop_list, (void *) &temp_scop))
ajScopDel(&temp_scop);
ajListFree(&scop_list);
ajListIterDel(&iter);
ajExit();
return 1;
}
/* Assign sequences in query file to sequence objects. */
qse = ajStrNew();
qss = ajStrNew();
while(ajReadlineTrim(ssin,&line))
{
/* SE string */
if(ajStrPrefixC(line,"SE"))
{
ajFmtScanS(line, "%*s %S", &qse);
/* Convert this string to 3-letter code & then convert to AjPSeq
object. */
q3se = ssematch_convertbases(qse);
}
/* SS string */
else if(ajStrPrefixC(line,"SS"))
{
while((ajReadlineTrim(ssin,&line)) && !ajStrPrefixC(line,"XX"))
ajStrAppendS(&qss,line);
ajStrRemoveWhite(&qss);
/* Convert this string to 3-letter code & then to AjPSeq object. */
q3ss = ssematch_convertbases(qss);
}
}
/* For se & then for ss, modes 0 & 1. */
for(mode = 0; mode <= 1; mode++)
{
/* Assign arguments for alignment function. */
if (mode == 0)
{
query = q3se;
gapopen = gapopen_sse;
gapextend = gapextend_sse;
outfile = out_se;
}
else if(mode == 1)
{
query = q3ss;
gapopen = gapopen_sss;
gapextend = gapextend_sss;
outfile = out_ss;
}
/* Iterate through list of scop objects & calculate alignment scores. */
iter=ajListIterNew(scop_list);
while((temp_scop=(AjPScop)ajListIterGet(iter)))
{
/* The function extracts the se (mode 0) or ss (mode 1) subject
sequences from the scop object, performs a Needleman-Wunsch
global alignment with the query sequence & allocates the score
to the Score element of the scop object*/
if(!(ssematch_NWScore(temp_scop , query, mode, matrix, gapopen, gapextend)))
{
ajFmtPrintF(logf, "%-15s\n", "ALIGNMENT");
ajFmtPrintF(logf, "Could not align sequence in scop domain %S\n ",
temp_scop->Entry);
ajFmtPrintS(&msg, "Could not align sequence in scop domain %S\n ",
temp_scop->Entry);
ajWarn(ajStrGetPtr(msg));
continue;
}
}
ajListIterDel(&iter);
temp_scop = NULL;
/* Sort list of Scop objects by Score */
ajListSort(scop_list, ssematch_CompScoreInv);
iter=ajListIterNew(scop_list);
/* Write top-scoring hits to outfile. */
for(x=0; x < max_hits; x++ )
{
temp_scop=(AjPScop)ajListIterGet(iter);
/* Print score to output file. */
ajFmtPrintF(outfile, "XX ALIGNMENT SCORE %.3f\nXX\n", temp_scop->Score);
/* Could also write alignment - later modification. */
if(!ajScopWrite(outfile, temp_scop))
ajFatal("Could not write output file %S\n", outfile);
}
ajListIterDel(&iter);
temp_scop = NULL;
}
/* Memoryt management. */
ajFileClose(&dcfin);
ajFileClose(&ssin);
ajMatrixfDel(&matrix);
ajFileClose(&out_ss);
ajFileClose(&out_se);
ajFileClose(&logf);
while(ajListPop(scop_list, (void *) &temp_scop))
ajScopDel(&temp_scop);
ajListFree(&scop_list);
ajStrDel(&msg);
ajStrDel(&line);
ajStrDel(&qse);
ajStrDel(&qss);
ajSeqDel(&q3se);
ajSeqDel(&q3ss);
ajExit();
return 0;
}