int main(int argc, char **argv)
{
/* ACD data item variables */
AjPFile hmmfile = NULL;
AjPSeqall seqfile = NULL;
AjBool nuc = 0;
ajint A = 0;
float E = 0.0;
float T = 0.0;
ajint Z = 0;
AjBool acc = ajFalse;
AjBool compat = ajFalse;
ajint cpu = 0;
AjBool cutga = ajFalse;
AjBool cuttc = ajFalse;
AjBool cutnc = ajFalse;
float dome = 0.0;
float domt = 0.0;
AjBool forward = ajFalse;
AjBool nulltwo = ajFalse;
AjBool pvm = ajFalse;
AjBool xnu = ajFalse;
AjPStr outname = NULL;
/* Housekeeping variables */
AjPStr cmd = NULL;
AjPStr rnd = NULL;
AjPSeqout rndo = NULL;
AjPSeq seq = NULL;
/* ACD file processing */
embInitPV("ehmmpfam",argc,argv,"HMMERNEW",VERSION);
hmmfile = ajAcdGetInfile("hmmfile");
seqfile = ajAcdGetSeqall("seqfile");
nuc = ajAcdGetBoolean("nuc");
A = ajAcdGetInt("A");
E = ajAcdGetFloat("E");
T = ajAcdGetFloat("T");
Z = ajAcdGetInt("Z");
acc = ajAcdGetBoolean("acc");
compat = ajAcdGetBoolean("compat");
cpu = ajAcdGetInt("cpu");
cutga = ajAcdGetBoolean("cutga");
cuttc = ajAcdGetBoolean("cuttc");
cutnc = ajAcdGetBoolean("cutnc");
dome = ajAcdGetFloat("dome");
domt = ajAcdGetFloat("domt");
forward = ajAcdGetBoolean("forward");
nulltwo = ajAcdGetBoolean("nulltwo");
pvm = ajAcdGetBoolean("pvm");
xnu = ajAcdGetBoolean("xnu");
outname = ajAcdGetOutfileName("outfile");
/* MAIN APPLICATION CODE */
/* 1. Housekeeping */
cmd = ajStrNew();
rnd = ajStrNew();
/* 2. Re-write seqfile to a temporary file in a format (fasta) HMMER can understand.
We cannot just pass the name of seqfile to HMMER as the name provided might be a
USA which HMMER would not understand. */
ajFilenameSetTempname(&rnd);
rndo = ajSeqoutNew();
if(!ajSeqoutOpenFilename(rndo, rnd))
ajFatal("Terminal ajSeqFileNewOut failure. Email EMBOSS helpdesk!\n");
ajSeqoutSetFormatC(rndo, "fasta");
while(ajSeqallNext(seqfile, &seq))
ajSeqoutWriteSeq(rndo, seq);
ajSeqoutClose(rndo);
ajSeqoutDel(&rndo);
/* 2. Build hmmpfam command line */
/* Command line is built in this order:
i. Application name.
ii. HMMER 'options' (in order they appear in ACD file)
iii.HMMER 'options' (that don't appear in ACD file)
iv. HMMER & new parameters.
*/
ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam"));
if(nuc)
ajStrAppendC(&cmd, " -n ");
ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z);
if(acc)
ajStrAppendC(&cmd, " --acc ");
if(compat)
ajStrAppendC(&cmd, " --compat ");
if(cpu)
ajFmtPrintAppS(&cmd, " --cpu %d ", cpu);
if(cutga)
ajStrAppendC(&cmd, " --cutga ");
if(cuttc)
ajStrAppendC(&cmd, " --cuttc ");
if(cutnc)
ajStrAppendC(&cmd, " --cutnc ");
ajFmtPrintAppS(&cmd, " --domE %f --domT %f ", dome, domt);
if(forward)
ajStrAppendC(&cmd, " --forward ");
if(nulltwo)
ajStrAppendC(&cmd, " --null2 ");
if(pvm)
ajStrAppendC(&cmd, " --pvm ");
if(xnu)
ajStrAppendC(&cmd, " --xnu ");
/* Note output redirected to outname.
rnd is the name of the rewritten seqfile.
MUST specify FASTA format explicitly. */
ajFmtPrintAppS(&cmd, " --informat FASTA %s %S",
ajFileGetNameC(hmmfile),
rnd);
/* 3. Close ACD files. */
ajFileClose(&hmmfile);
ajSeqallDel(&seqfile);
/* 4. Call hmmpfam. Use C system call instead of ajSystem
so that redirect in cmd works ok. */
ajFmtPrint("\n%S\n\n", cmd);
ajSysExecOutnameAppendS(cmd,outname);
/* 5. Exit cleanly */
ajSysFileUnlinkS(rnd);
ajStrDel(&cmd);
ajStrDel(&rnd);
ajStrDel(&outname);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqset seqset = NULL;
AjPStr cl = NULL;
AjPSeqout seqout = NULL;
AjBool full = ajFalse;
AjPStr fn = NULL;
AjPStr stmp = NULL;
AjPStr outfname = NULL;
embInitPV("echlorop", argc, argv, "CBSTOOLS", VERSION);
seqset = ajAcdGetSeqset("sequence");
outfname= ajAcdGetOutfileName("outfile");
full = ajAcdGetBoolean("full");
cl = ajStrNewS(ajAcdGetpathC("chlorop"));
fn = ajStrNew();
stmp = ajStrNew();
ajFilenameSetTempname(&fn);
seqout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(seqout, fn))
ajFatal("Cannot open temporary file %S",fn);
ajSeqoutSetFormatC(seqout, "fasta");
ajSeqoutWriteSet(seqout,seqset);
ajSeqoutClose(seqout);
if(full)
ajStrAppendC(&cl," -F");
ajFmtPrintS(&stmp," %S",fn);
ajStrAppendS(&cl,stmp);
#if 0
ajFmtPrint("%S\n",cl);
#endif
#if 1
ajSysExecOutnameAppendS(cl, outfname);
#endif
ajSysFileUnlinkS(fn);
ajStrDel(&cl);
ajStrDel(&fn);
ajStrDel(&stmp);
ajSeqoutDel(&seqout);
ajSeqsetDel(&seqset);
ajStrDel(&outfname);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqset seqset = NULL;
AjPStr cl = NULL;
AjPSeqout seqout = NULL;
float thresh = 0.;
AjBool netphos = ajFalse;
AjPStr format = NULL;
AjBool plot = ajFalse;
AjPStr fn = NULL;
AjPStr stmp = NULL;
AjPStr outfname = NULL;
embInitPV("eyinoyang", argc, argv, "CBSTOOLS",VERSION);
seqset = ajAcdGetSeqset("sequence");
outfname= ajAcdGetOutfileName("outfile");
plot = ajAcdGetBoolean("plot");
netphos = ajAcdGetBoolean("netphos");
thresh = ajAcdGetFloat("threshold");
format = ajAcdGetListSingle("format");
cl = ajStrNewS(ajAcdGetpathC("yinOyang"));
fn = ajStrNew();
stmp = ajStrNew();
ajFilenameSetTempname(&fn);
seqout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(seqout, fn))
ajFatal("Cannot open temporary file %S",fn);
ajSeqoutSetFormatC(seqout, "fasta");
ajSeqoutWriteSet(seqout,seqset);
ajSeqoutClose(seqout);
if(ajStrMatchC(format,"short"))
ajStrAppendC(&cl," -f s");
else if(ajStrMatchC(format,"long"))
ajStrAppendC(&cl," -f l");
if(plot)
ajStrAppendC(&cl," -g");
if(netphos)
ajStrAppendC(&cl," -y");
if(netphos)
{
ajFmtPrintS(&stmp," -t %f",thresh);
ajStrAppendS(&cl,stmp);
}
ajFmtPrintS(&stmp," %S",fn);
ajStrAppendS(&cl,stmp);
#if 0
ajFmtPrint("%`S\n",cl);
#endif
#if 1
ajSysExecOutnameAppendS(cl, outfname);
#endif
ajSysFileUnlinkS(fn);
ajStrDel(&cl);
ajStrDel(&fn);
ajStrDel(&stmp);
ajStrDel(&format);
ajSeqoutDel(&seqout);
ajSeqsetDel(&seqset);
ajStrDel(&outfname);
embExit();
return 0;
}
