AjBool gGetFileContent(AjPStr* content, AjPStr filename){
AjPFile file = NULL;
AjPStr line = NULL;
if((file = ajFileNewInNameS(filename)) == NULL)
return ajFalse;
while(ajReadline(file, &line))
ajStrAppendS(content, line);
if(file)
ajFileClose(&file);
ajSysFileUnlinkS(filename);
return ajTrue;
}
int main(int argc, char *argv[])
{
embInitPV("ggeneskew", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
ajint window = 0;
ajint slide = 0;
AjBool cumulative = ajFalse;
AjBool gc3 = ajFalse;
AjPStr basetype = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
seqall = ajAcdGetSeqall("sequence");
window = ajAcdGetInt("window");
slide = ajAcdGetInt("slide");
cumulative = ajAcdGetBoolean("cumulative");
gc3 = ajAcdGetBoolean("gctri");
basetype = ajAcdGetSelectSingle("base");
accid = ajAcdGetBoolean("accid");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
if(ajStrMatchC(base, "none"))
basetype = ajStrNewC("");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
gAssignUniqueName(&tmpname);
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajFmtError("Output file (%S) open error\n", tmpname);
embExitBad();
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajFmtError("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
if(accid)
{
ajStrAssignS(&restid, seqid);
if(ajStrGetLen(seqid) == 0)
{
ajDie("Cannot proceed without header with -accid\n");
}
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/geneskew/window=%d/slide=%d/"
"cumulative=%d/gc3=%d/base=%S/output=f/tag=gene",
base, restid, window, slide, cumulative, gc3, basetype);
if(plot)
{
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("gene skew");
gpp.ylab = ajStrNewC("bp");
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
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[])
{
embInitPV("gviewcds", argc, argv, "GEMBASSY", "1.0.1");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
ajint length = 0;
ajint gap = 0;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
AjPPStr names = NULL;
ajint i;
seqall = ajAcdGetSeqall("sequence");
length = ajAcdGetInt("length");
gap = ajAcdGetInt("gap");
accid = ajAcdGetBoolean("accid");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
gAssignUniqueName(&tmpname);
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajFmtError("Output file (%S) open error\n", tmpname);
embExitBad();
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajFmtError("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
if(accid)
{
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(!ajStrGetLen(seqid))
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(!ajStrGetLen(seqid))
{
ajFmtError("No valid header information\n");
embExitBad();
}
ajStrAssignS(&restid, seqid);
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/view_cds/length=%d/gap=%d/"
"output=f/tag=gene", base, restid, length, gap);
if(plot)
{
if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
ajDie("Error in memory allocation, exiting\n");
}
names[0] = NULL;
names[1] = ajStrNewC("A");
names[2] = ajStrNewC("T");
names[3] = ajStrNewC("G");
names[4] = ajStrNewC("C");
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("position");
gpp.ylab = ajStrNewC("percentage");
gpp.names = names;
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
i = 0;
while(names[i])
{
AJFREE(names[i]);
++i;
}
AJFREE(names);
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gp2", argc, argv, "GEMBASSY", "1.0.1");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
accid = ajAcdGetBoolean("accid");
outf = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajDie("Output file (%S) open error\n", tmpname);
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajDie("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
if(accid)
{
ajStrAssignS(&restid, ajSeqGetAccS(seq));
if(!ajStrGetLen(restid))
{
ajStrAssignS(&restid, ajSeqGetNameS(seq));
}
if(!ajStrGetLen(restid))
{
ajDie("No valid header information\n");
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/P2/output=f/tag=gene", base, restid);
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajStrDel(&url);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
int main(int argc, char **argv) {
embInitPV("kdnapenny", argc, argv, "KBWS", "1.0.8");
struct soap soap;
char* jobid;
char* result;
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPStr substr;
AjPStr inseq = NULL;
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
AjPStr tmp = NULL;
AjPStr tmpFileName = NULL;
AjPSeqout fil_file;
AjPStr line = NULL;
AjPStr sizestr = NULL;
ajint thissize = 0;
ajint nb = 0;
AjBool are_prot = ajFalse;
ajint size = 0;
AjPFile infile;
tmp = ajStrNewC("fasta");
fil_file = ajSeqoutNew();
tmpFileName = getUniqueFileName();
if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(inseq);
if ( soap_call_ns1__runDnapenny( &soap, NULL, NULL, in0, &jobid ) == SOAP_OK ) {
fprintf(stderr,"Jobid: %s\n",jobid);
} else {
soap_print_fault(&soap, stderr);
}
int check = 0;
while ( check == 0 ) {
if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid, &check ) == SOAP_OK ) {
fprintf(stderr,"*");
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
fprintf(stderr, "\n");
if ( soap_call_ns1__getResult( &soap, NULL, NULL, jobid, &result ) == SOAP_OK ) {
substr = ajStrNewC(result);
ajFmtPrintF(outf,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
ajSysFileUnlinkS(tmpFileName);
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
embExit();
return 0;
}
int main(int argc, char **argv) {
embInitPV("kmafft", argc, argv, "KBWS", "1.0.8");
struct soap soap;
struct ns1__mafftInputParams params;
char* jobid;
char* result;
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPStr substr;
AjPStr inseq = NULL;
AjPStr strategy;
AjPStr outorder;
float op;
float ep;
AjPStr scorematrix;
AjBool homologs;
AjBool showhomologs;
float threshold;
AjPStr referenceseq;
AjPStr harrplot;
strategy = ajAcdGetString("strategy");
outorder = ajAcdGetString("outorder");
op = ajAcdGetFloat("op");
ep = ajAcdGetFloat("ep");
scorematrix = ajAcdGetString("scorematrix");
homologs = ajAcdGetBoolean("homologs");
showhomologs = ajAcdGetBoolean("showhomologs");
threshold = ajAcdGetFloat("threshold");
referenceseq = ajAcdGetString("referenceseq");
harrplot = ajAcdGetString("harrplot");
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
params.strategy = ajCharNewS(strategy);
params.outorder = ajCharNewS(outorder);
params.op = op;
params.ep = ep;
params.scorematrix = ajCharNewS(scorematrix);
if (homologs) {
params.homologs = xsd__boolean__true_;
} else {
params.homologs = xsd__boolean__false_;
}
if (showhomologs) {
params.showhomologs = xsd__boolean__true_;
} else {
params.showhomologs = xsd__boolean__false_;
}
params.threshold = threshold;
params.referenceseq = ajCharNewS(referenceseq);
params.harrplot = ajCharNewS(harrplot);
AjPStr tmp = NULL;
AjPStr tmpFileName = NULL;
AjPSeqout fil_file;
AjPStr line = NULL; /* if "AjPStr line; -> ajReadline is not success!" */
AjPStr sizestr = NULL;
ajint thissize;
ajint nb = 0;
AjBool are_prot = ajFalse;
ajint size = 0;
AjPFile infile;
tmp = ajStrNewC("fasta");
fil_file = ajSeqoutNew();
tmpFileName = getUniqueFileName();
if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(inseq);
if ( soap_call_ns1__runMafft( &soap, NULL, NULL, in0, ¶ms, &jobid ) == SOAP_OK ) {
fprintf(stderr,"Jobid: %s\n",jobid);
} else {
soap_print_fault(&soap, stderr);
}
int check = 0;
while ( check == 0 ) {
if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid, &check ) == SOAP_OK ) {
fprintf(stderr,"*");
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
fprintf(stderr,"\n");
if ( soap_call_ns1__getResult( &soap, NULL, NULL, jobid, &result ) == SOAP_OK ) {
substr = ajStrNewC(result);
ajFmtPrintF(outf,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
ajSysFileUnlinkS(tmpFileName);
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
embExit();
return 0;
}
int main(int argc, char **argv) {
// initialize EMBASSY info
embInitPV("kweblogo", argc, argv, "KBWS", "1.0.9");
// soap driver and parameter object
struct soap soap;
struct ns1__weblogoInputParams params;
char* jobid;
AjPSeqall seqall;
AjPSeq seq;
AjPStr substr;
AjPStr inseq = NULL;
// get input sequence
seqall= ajAcdGetSeqall("seqall");
// get/set parameters
params.format = ajCharNewS(ajAcdGetString("format"));
AjPStr tmp= NULL;
AjPStr tmpFileName= NULL;
AjPSeqout fil_file;
AjPStr line= NULL; /* if "AjPStr line; -> ajReadline is not success!" */
AjPStr sizestr= NULL;
ajint thissize;
ajint nb= 0;
AjBool are_prot= ajFalse;
ajint size= 0;
AjPFile infile;
AjPFile goutf;
AjPStr goutfile;
goutfile= ajAcdGetString("goutfile");
tmp= ajStrNewC("fasta");
fil_file= ajSeqoutNew();
tmpFileName= getUniqueFileName();
if(!ajSeqoutOpenFilename(fil_file, tmpFileName)) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0= ajCharNewS(inseq);
if (soap_call_ns1__runWeblogo( &soap, NULL, NULL, in0, ¶ms, &jobid) == SOAP_OK) {
} else {
soap_print_fault(&soap, stderr);
}
int check= 0;
while (check == 0 ) {
if (soap_call_ns1__checkStatus(&soap, NULL, NULL, jobid, &check) == SOAP_OK) {
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
char* image_url;
if (soap_call_ns1__getResult(&soap, NULL, NULL, jobid, &image_url) == SOAP_OK) {
goutf= ajFileNewOutNameS(goutfile);
if (!goutf) {
// can not open image output file
ajFmtError("Problem writing out image file");
embExitBad();
}
if (!gHttpGetBinC(image_url, &goutf)) {
// can not download image file
ajFmtError("Problem downloading image file");
embExitBad();
}
} else {
soap_print_fault(&soap, stderr);
}
// delete temporary multi-fasta sequence file
ajSysFileUnlinkS(tmpFileName);
// destruct SOAP driver
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
// destruct EMBOSS object
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
// exit
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gseqinfo", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr ori = NULL;
AjPStr ter = NULL;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPStr tmpname = NULL;
AjPSeqout tmpout = NULL;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
outf = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
ajStrAppendC(&tmpname, ".fasta");
while(ajSeqallNext(seqall, &seq))
{
tmpout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(tmpout, tmpname))
{
embExitBad();
}
ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
ajSeqoutWriteSeq(tmpout, seq);
ajSeqoutClose(tmpout);
ajSeqoutDel(&tmpout);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/seqinfo/", base, restid);
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* ACD data item variables */
AjPFile hmmfile = NULL;
AjPSeqset seqfile = NULL;
AjPFile mapali = NULL;
AjPFile withali = NULL;
AjPAlign o = NULL;
AjBool m = ajFalse;
AjBool q = ajFalse;
/* Housekeeping variables */
AjPStr cmd = NULL;
AjPStr fmt = NULL;
AjBool fmtok = ajFalse;
AjPStr rnd = NULL;
AjPSeqout rndo = NULL;
/* ACD file processing */
embInitPV("ehmmalign",argc,argv,"HMMERNEW",VERSION);
hmmfile = ajAcdGetInfile("hmmfile");
seqfile = ajAcdGetSeqset("seqfile");
mapali = ajAcdGetInfile("mapali");
withali = ajAcdGetInfile("withali");
o = ajAcdGetAlign("o");
m = ajAcdGetBoolean("m");
q = ajAcdGetBoolean("q");
/* MAIN APPLICATION CODE */
/* 1. Housekeeping */
cmd = ajStrNew();
fmt = 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");
ajSeqoutWriteSet(rndo, seqfile);
ajSeqoutClose(rndo);
ajSeqoutDel(&rndo);
/* 3. Build hmmalign 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.
*/
ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign"));
if(mapali)
ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali));
if(withali)
ajFmtPrintAppS(&cmd, " --withali %s ", ajFileGetNameC(withali));
if(m)
ajStrAppendC(&cmd, " -m ");
if(q)
ajStrAppendC(&cmd, " -q ");
/* Ensure output alignment is in user-specified format. */
fmtok=ajTrue;
ajStrAssignS(&fmt, ajAlignGetFormat(o));
/* fasta and a2m are identical formats. */
if(ajStrMatchC(fmt, "fasta"))
ajStrAssignC(&fmt, "A2M");
else if(ajStrMatchC(fmt, "a2m"))
ajStrAssignC(&fmt, "A2M");
else if(ajStrMatchC(fmt, "msf"))
ajStrAssignC(&fmt, "MSF");
else if(ajStrMatchC(fmt, "phylip"))
ajStrAssignC(&fmt, "PHYLIP");
/* hmmer also supports stockholm, SELEX & Clustal output, EMBOSS does not.
EMBOSS supports unknown/multiple/simple and srs output, hmmer does not. */
else
fmtok = ajFalse;
if(!fmtok)
{
/* This could be replaced with code to reformat the file. */
ajWarn("Specified output alignment format ('o' ACD option) is "
"not understood by HMMER. Using stockholm format instead.");
ajStrAssignC(&fmt, "Stockholm");
}
/* rnd is the name of the rewritten seqfile. MUST specify FASTA format explicitly. */
ajFmtPrintAppS(&cmd, " --informat FASTA --outformat %S -o %s %s %S",
fmt,
ajAlignGetFilename(o),
ajFileGetNameC(hmmfile),
rnd);
/* 4. Close ACD files */
ajFileClose(&hmmfile);
ajSeqsetDel(&seqfile);
ajFileClose(&mapali);
ajFileClose(&withali);
ajAlignClose(o);
ajAlignDel(&o);
/* 5. Call hmmalign */
ajFmtPrint("\n%S\n\n", cmd);
ajSysExecS(cmd);
/* 6. Exit cleanly */
ajSysFileUnlinkS(rnd);
ajStrDel(&cmd);
ajStrDel(&fmt);
ajStrDel(&rnd);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("greporiter", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjBool oriloc = 0;
AjBool gcskew = 0;
AjBool dbonly = 0;
ajint difthreshold = 0;
AjPFile outf = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjPStr fstname = NULL;
AjPFilebuff tmp = NULL;
AjPStr line = NULL;
AjPSeqout tmpout = NULL;
AjPRegexp regex;
AjPStr ori = NULL;
AjPStr ter = NULL;
seqall = ajAcdGetSeqall("sequence");
difthreshold = ajAcdGetInt("difthreshold");
oriloc = ajAcdGetBoolean("oriloc");
gcskew = ajAcdGetBoolean("gcskew");
dbonly = ajAcdGetBoolean("dbonly");
accid = ajAcdGetBoolean("accid");
outf = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
gAssignUniqueName(&fstname);
ajStrAppendC(&fstname, ".fasta");
while(ajSeqallNext(seqall, &seq))
{
inseq = ajStrNew();
tmpout = ajSeqoutNew();
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajDie("Output file (%S) open error\n", tmpname);
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
if(!ajSeqoutOpenFilename(tmpout, fstname))
{
embExitBad();
}
ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
ajSeqoutWriteSeq(tmpout, seq);
ajSeqoutClose(tmpout);
ajSeqoutDel(&tmpout);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, fstname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(fstname);
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
if(accid)
{
ajStrAssignS(&restid, seqid);
if(ajStrGetLen(seqid) == 0)
{
ajDie("Cannot proceed without header with -accid\n");
}
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/rep_ori_ter/oriloc=%d/gcskew=%d/"
"difthreshold=%d/dbonly=%d/", base, restid, oriloc, gcskew,
difthreshold, dbonly);
if(!gFilebuffURLS(url, &tmp))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajBuffreadLine(tmp, &line);
regex = ajRegCompC("([0-9]+),([0-9]+)");
if(ajRegExec(regex, line)) {
if(ajRegSubI(regex, 1, &ori), ajRegSubI(regex, 2, &ter)) {
ajFmtPrint("%S Origin: %S Terminus %S\n", seqid, ori, ter);
}
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
AjBool gFormatGenbank(AjPSeq seq, AjPStr *inseq){
AjPSeqout seqout = NULL;
AjPFeattabOut featout = NULL;
AjPFeattable feat = NULL;
AjPStr seqline = NULL;
AjPStr featline = NULL;
AjPFile seqfile = NULL;
AjPFile featfile = NULL;
AjPStr filename = NULL;
AjBool hasfeats = ajTrue;
gAssignUniqueName(&filename);
feat = ajSeqGetFeatCopy(seq);
if(!feat) {
hasfeats = ajFalse;
}
seqout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(seqout,filename))
embExitBad();
ajSeqoutSetFormatS(seqout,ajStrNewC("genbank"));
ajSeqoutWriteSeq(seqout,seq);
ajSeqoutClose(seqout);
ajSeqoutDel(&seqout);
seqfile = ajFileNewInNameS(filename);
ajSysFileUnlinkS(filename);
if(hasfeats) {
featout = ajFeattabOutNew();
if(!ajFeattabOutOpen(featout,filename))
return ajFalse;
ajFeattableWriteGenbank(featout,feat);
ajFeattableDel(&feat);
//ajFeattabOutDel(&featout);
ajFileClose(&(featout->Handle));
featfile = ajFileNewInNameS(filename);
ajSysFileUnlinkS(filename);
}
while(ajReadline(seqfile,&seqline)){
if(hasfeats && ajStrMatchC(seqline,"ORIGIN\n")){
while(ajReadline(featfile,&featline)){
ajStrAppendS(inseq, featline);
}
}
ajStrAppendS(inseq, seqline);
}
ajStrDel(&seqline);
ajStrDel(&featline);
ajStrDel(&filename);
ajFileClose(&seqfile);
ajFileClose(&featfile);
return hasfeats;
}
int main(int argc, char **argv) {
embInitPV("kclustalw", argc, argv, "KBWS", "1.0.8");
struct soap soap;
struct ns1__clustalwInputParams params;
char* jobid;
char* result;
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPFile outf_dnd;
AjPStr substr;
AjPStr inseq = NULL;
AjPStr alignment;
AjPStr output;
AjPStr matrix;
AjPStr outorder;
ajint ktup;
ajint window;
ajint gapopen;
float gapext;
ajint gapdist;
AjBool endgaps;
ajint pairgap;
ajint topdiags;
AjPStr score;
AjBool tossgaps;
AjBool kimura;
AjPStr outputtree;
AjBool tree;
AjBool quicktree;
AjBool align;
AjPStr clustering;
ajint numiter;
AjPStr iteration;
alignment = ajAcdGetString("alignment");
output = ajAcdGetString("output");
matrix = ajAcdGetString("matrix");
outorder = ajAcdGetString("outorder");
ktup = ajAcdGetInt("ktup");
window = ajAcdGetInt("window");
gapopen = ajAcdGetInt("gapopen");
gapext = ajAcdGetFloat("gapext");
gapdist = ajAcdGetInt("gapdist");
endgaps = ajAcdGetBoolean("endgaps");
pairgap = ajAcdGetInt("pairgap");
topdiags = ajAcdGetInt("topdiags");
score = ajAcdGetString("score");
tossgaps = ajAcdGetBoolean("tossgaps");
kimura = ajAcdGetBoolean("kimura");
outputtree = ajAcdGetString("outputtree");
tree = ajAcdGetBoolean("tree");
quicktree = ajAcdGetBoolean("quicktree");
align = ajAcdGetBoolean("align");
clustering = ajAcdGetString("clustering");
numiter = ajAcdGetInt("numiter");
iteration = ajAcdGetString("iteration");
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
outf_dnd = ajAcdGetOutfile("dndoutfile");
params.alignment = ajCharNewS(alignment);
params.output = ajCharNewS(output);
params.matrix = ajCharNewS(matrix);
params.outorder = ajCharNewS(outorder);
params.ktup = ktup;
params.window = window;
params.gapopen = gapopen;
params.gapext = gapext;
params.gapdist = gapdist;
if (endgaps) {
params.endgaps = xsd__boolean__true_;
} else {
params.endgaps = xsd__boolean__false_;
}
params.pairgap = pairgap;
params.topdiags = topdiags;
params.score = ajCharNewS(score);
if (tossgaps) {
params.tossgaps = xsd__boolean__true_;
} else {
params.tossgaps = xsd__boolean__false_;
}
if (kimura) {
params.kimura = xsd__boolean__true_;
} else {
params.kimura = xsd__boolean__false_;
}
params.outputtree = ajCharNewS(outputtree);
if (tree) {
params.tree = xsd__boolean__true_;
} else {
params.tree = xsd__boolean__false_;
}
if (quicktree) {
params.quicktree = xsd__boolean__true_;
} else {
params.quicktree = xsd__boolean__false_;
}
if (align) {
params.align = xsd__boolean__true_;
} else {
params.align = xsd__boolean__false_;
}
params.clustering = ajCharNewS(clustering);
params.numiter = numiter;
params.iteration = ajCharNewS(iteration);
AjPStr tmp = NULL;
AjPStr tmpFileName = NULL;
AjPSeqout fil_file;
AjPStr line = NULL; /* if "AjPStr line; -> ajReadline is not success!" */
AjPStr sizestr = NULL;
ajint thissize;
ajint nb = 0;
AjBool are_prot = ajFalse;
ajint size = 0;
AjPFile infile;
tmp = ajStrNewC("fasta");
fil_file = ajSeqoutNew();
tmpFileName = getUniqueFileName();
if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(inseq);
if ( soap_call_ns1__runClustalw( &soap, NULL, NULL, in0, ¶ms, &jobid ) == SOAP_OK ) {
fprintf(stderr,"Jobid: %s\n",jobid);
} else {
soap_print_fault(&soap, stderr);
}
int check = 0;
while ( check == 0 ) {
if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid, &check ) == SOAP_OK ) {
fprintf(stderr,"*");
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
fprintf(stderr,"\n");
char* type;
type = "out";
if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
substr = ajStrNewC(result);
fprintf(stdout, "%s\n", ajStrGetPtr(substr));
} else {
soap_print_fault(&soap, stderr);
}
type = "aln";
if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
substr = ajStrNewC(result);
ajFmtPrintF(outf,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
type = "dnd";
if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
substr = ajStrNewC(result);
ajFmtPrintF(outf_dnd,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
ajSysFileUnlinkS(tmpFileName);
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf_dnd);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("goligomersearch", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr oligomer = NULL;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPStr _return = NULL;
AjPStr tmpname = NULL;
AjPSeqout tmpout = NULL;
AjPFilebuff tmp = NULL;
AjPStr line = NULL;
AjPFile outfile = NULL;
seqall = ajAcdGetSeqall("sequence");
oligomer = ajAcdGetString("oligomer");
_return = ajAcdGetSelectSingle("return");
outfile = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
ajStrAppendC(&tmpname, ".fasta");
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
tmpout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(tmpout, tmpname))
{
embExitBad();
}
ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
ajSeqoutWriteSeq(tmpout, seq);
ajSeqoutClose(tmpout);
ajSeqoutDel(&tmpout);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/oligomer_search/%S/return=%S",
base, restid, oligomer, _return);
if(!gFilebuffURLS(url, &tmp))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajBuffreadLine(tmp, &line);
ajStrRemoveSetC(&line, "\n");
ajFmtPrintF(outfile, "Sequence: %S Oligomer: %S Return: %S\n",
seqid, oligomer, line);
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outfile);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
ajStrDel(&oligomer);
embExit();
return 0;
}
/* @funcstatic domainalign_stamp **********************************************
**
** Call STAMP and process files.
**
** @param [r] prevdomain [AjPDomain] Previous domain.
** @param [r] domain [AjPDomain] This domain.
** @param [r] daf [AjPDirout] Domain alignment files.
** @param [r] super [AjPDirout] Superimposition files.
** @param [r] singlets [AjPDirout] Singlet files.
** @param [r] align [AjPStr] Align.
** @param [r] alignc [AjPStr] Alignc.
** @param [r] dom [AjPStr] Dom.
** @param [r] name [AjPStr] Name.
** @param [r] set [AjPStr] Name of set file.
** @param [r] scan [AjPStr] Name of scan file.
** @param [r] sort [AjPStr] Name of sort file.
** @param [r] log [AjPStr] Log file name.
** @param [r] out [AjPStr] Out file name.
** @param [r] keepsinglets [AjBool] Keep singlet sequences or not.
** @param [r] moden [ajint] Mode number.
** @param [r] noden [ajint] Node number.
** @param [r] nset [ajint] Number in set.
** @param [r] logf [AjPFile] Lof file.
**
**
** @return [void] True on success
** @@
****************************************************************************/
static void domainalign_stamp(AjPDomain prevdomain,
AjPDomain domain,
AjPDirout daf,
AjPDirout super,
AjPDirout singlets,
AjPStr align,
AjPStr alignc,
AjPStr dom,
AjPStr name,
AjPStr set,
AjPStr scan,
AjPStr sort,
AjPStr log,
AjPStr out,
AjBool keepsinglets,
ajint moden,
ajint noden,
ajint nset,
AjPFile logf)
{
AjPStr exec = NULL; /* The UNIX command line to be executed. */
AjPFile clusterf = NULL; /* File pointer for log file. */
ajint ncluster = 0; /* Counter for the number of clusters. */
AjPStr line = NULL; /* Holds a line from the log file. */
AjPRegexp rexp = NULL; /* For parsing no. of clusters in log file */
AjPStr temp = NULL; /* A temporary string. */
ajint x = 0; /* Loop counter. */
exec = ajStrNew();
line = ajStrNew();
temp = ajStrNew();
rexp = ajRegCompC("^(Cluster:)");
ajDebug("domainalign_stamp name: '%S'\n", name);
/* Call STAMP. */
ajFmtPrintS(&exec, "%S -l %S -s -n 2 -slide 5 -prefix %S -d %S",
ajAcdGetpathC("stamp"), dom, name, set);
ajFmtPrint("\n%S\n\n", exec);
ajSysExecS(exec);
ajFmtPrintS(&exec, "%S -f %S -s Sc 2.5",
ajAcdGetpathC("sorttrans"), scan);
ajFmtPrint("\n%S > %S\n\n", exec, sort);
ajSysExecOutnameS(exec, sort);
ajFmtPrintS(&exec, "%S -l %S -prefix %S",
ajAcdGetpathC("stamp"), sort, name);
ajFmtPrint("\n%S > %S\n\n", exec, log);
ajSysExecOutnameS(exec, log);
ajFmtPrintS(&exec, "%S -f %S -g -o %S",
ajAcdGetpathC("transform"), sort, alignc);
ajFmtPrint("\n%S\n\n", exec);
ajSysExecS(exec);
/* Count the number of clusters in the log file. */
if(!(clusterf=ajFileNewInNameS(log)))
ajFatal("Could not open log file '%S'\n", log);
ncluster=0;
while(ajReadlineTrim(clusterf,&line))
if(ajRegExec(rexp,line))
ncluster++;
ajFileClose(&clusterf);
ajDebug("ncluster: %d\n", ncluster);
/* Call STAMP ... calculate two fields for structural equivalence using
threshold Pij value of 0.5, see stamp manual v4.1 pg 27. */
ajFmtPrintS(&exec,"%S -f %S.%d -min 0.5",
ajAcdGetpathC("poststamp"), name, ncluster);
ajFmtPrint("%S\n\n", exec);
ajSysExecS(exec);
/* Call STAMP ... convert block format alignment into clustal format. */
ajFmtPrintS(&exec,"%S -f %S.%d.post",
ajAcdGetpathC("ver2hor"), name, ncluster);
ajFmtPrint("%S > %S\n\n", exec, out);
ajSysExecOutnameS(exec, out);
/* Process STAMP alignment file and generate alignment file for output. */
domainalign_ProcessStampFile(out, align, prevdomain, noden, logf);
/* Remove all temporary files. */
for(x=1;x<ncluster+1;x++)
{
ajFmtPrintS(&temp, "%S.%d", name, x);
ajSysFileUnlinkS(temp);
}
ajFmtPrintS(&temp, "%S.%d.post", name, ncluster);
ajSysFileUnlinkS(temp);
ajStrDel(&exec);
ajStrDel(&line);
ajStrDel(&temp);
ajRegFree(&rexp);
return;
}
int main(int argc, char **argv)
{
AjPSeqall seqall = NULL;
AjPFile dend_outfile = NULL;
AjPStr tmp_dendfilename = NULL;
AjPFile tmp_dendfile = NULL;
AjPStr tmp_aln_outfile = NULL;
AjPSeqset seqset = NULL;
AjPSeqout seqout = NULL;
AjPSeqin seqin = NULL;
AjBool only_dend;
AjBool are_prot = ajFalse;
AjBool do_slow;
AjBool use_dend;
AjPFile dend_file = NULL;
AjPStr dend_filename = NULL;
ajint ktup;
ajint gapw;
ajint topdiags;
ajint window;
AjBool nopercent;
AjPStr pw_matrix = NULL;
AjPStr pw_dna_matrix = NULL;
AjPFile pairwise_matrix = NULL;
float pw_gapc;
float pw_gapv;
AjPStr pwmstr = NULL;
char pwmc = '\0';
AjPStr pwdstr = NULL;
char pwdc = '\0';
AjPStr m1str = NULL;
AjPStr m2str = NULL;
char m1c = '\0';
char m2c = '\0';
AjPStr matrix = NULL;
AjPStr dna_matrix = NULL;
AjPFile ma_matrix = NULL;
float gapc;
float gapv;
AjBool endgaps;
AjBool norgap;
AjBool nohgap;
ajint gap_dist;
ajint maxdiv;
AjPStr hgapres = NULL;
AjPSeqout fil_file = NULL;
AjPSeq seq = NULL;
AjPStr cmd = NULL;
AjPStr tmp = NULL;
AjPStr tmpFilename;
AjPStr line = NULL;
ajint nb = 0;
/* get all the parameters */
embInit("emma", argc, argv);
pwmstr = ajStrNew();
pwdstr = ajStrNew();
m1str = ajStrNew();
m2str = ajStrNew();
seqall = ajAcdGetSeqall("sequence");
seqout = ajAcdGetSeqoutset("outseq");
dend_outfile = ajAcdGetOutfile("dendoutfile");
only_dend = ajAcdGetToggle("onlydend");
use_dend = ajAcdGetToggle("dendreuse");
dend_file = ajAcdGetInfile("dendfile");
if (dend_file)
ajStrAssignS(&dend_filename, ajFileGetPrintnameS(dend_file));
ajFileClose(&dend_file);
do_slow = ajAcdGetToggle("slowalign");
ktup = ajAcdGetInt("ktup");
gapw = ajAcdGetInt("gapw");
topdiags = ajAcdGetInt("topdiags");
window = ajAcdGetInt("window");
nopercent = ajAcdGetBoolean("nopercent");
pw_matrix = ajAcdGetListSingle("pwmatrix");
pwmc = ajStrGetCharFirst(pw_matrix);
if(pwmc=='b')
ajStrAssignC(&pwmstr,"blosum");
else if(pwmc=='p')
ajStrAssignC(&pwmstr,"pam");
else if(pwmc=='g')
ajStrAssignC(&pwmstr,"gonnet");
else if(pwmc=='i')
ajStrAssignC(&pwmstr,"id");
else if(pwmc=='o')
ajStrAssignC(&pwmstr,"own");
pw_dna_matrix = ajAcdGetListSingle("pwdnamatrix");
pwdc = ajStrGetCharFirst(pw_dna_matrix);
if(pwdc=='i')
ajStrAssignC(&pwdstr,"iub");
else if(pwdc=='c')
ajStrAssignC(&pwdstr,"clustalw");
else if(pwdc=='o')
ajStrAssignC(&pwdstr,"own");
pairwise_matrix = ajAcdGetInfile("pairwisedatafile");
pw_gapc = ajAcdGetFloat( "pwgapopen");
pw_gapv = ajAcdGetFloat( "pwgapextend");
matrix = ajAcdGetListSingle( "matrix");
m1c = ajStrGetCharFirst(matrix);
if(m1c=='b')
ajStrAssignC(&m1str,"blosum");
else if(m1c=='p')
ajStrAssignC(&m1str,"pam");
else if(m1c=='g')
ajStrAssignC(&m1str,"gonnet");
else if(m1c=='i')
ajStrAssignC(&m1str,"id");
else if(m1c=='o')
ajStrAssignC(&m1str,"own");
dna_matrix = ajAcdGetListSingle( "dnamatrix");
m2c = ajStrGetCharFirst(dna_matrix);
if(m2c=='i')
ajStrAssignC(&m2str,"iub");
else if(m2c=='c')
ajStrAssignC(&m2str,"clustalw");
else if(m2c=='o')
ajStrAssignC(&m2str,"own");
ma_matrix = ajAcdGetInfile("mamatrixfile");
gapc = ajAcdGetFloat("gapopen");
gapv = ajAcdGetFloat("gapextend");
endgaps = ajAcdGetBoolean("endgaps");
norgap = ajAcdGetBoolean("norgap");
nohgap = ajAcdGetBoolean("nohgap");
gap_dist = ajAcdGetInt("gapdist");
hgapres = ajAcdGetString("hgapres");
maxdiv = ajAcdGetInt("maxdiv");
tmp = ajStrNewC("fasta");
/*
** Start by writing sequences into a unique temporary file
** get file pointer to unique file
*/
fil_file = ajSeqoutNew();
tmpFilename = emma_getUniqueFileName();
if(!ajSeqoutOpenFilename( fil_file, tmpFilename))
embExitBad();
/* Set output format to fasta */
ajSeqoutSetFormatS( fil_file, tmp);
while(ajSeqallNext(seqall, &seq))
{
/*
** Check sequences are all of the same type
** Still to be done
** Write out sequences
*/
if (!nb)
are_prot = ajSeqIsProt(seq);
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
if(nb < 2)
ajFatal("Multiple alignments need at least two sequences");
/* Generate clustalw command line */
cmd = ajStrNewS(ajAcdGetpathC("clustalw"));
/* add tmp file containing sequences */
ajStrAppendC(&cmd, " -infile=");
ajStrAppendS(&cmd, tmpFilename);
/* add out file name */
tmp_aln_outfile = emma_getUniqueFileName();
ajStrAppendC(&cmd, " -outfile=");
ajStrAppendS(&cmd, tmp_aln_outfile);
/* calculating just the nj tree or doing full alignment */
if(only_dend)
ajStrAppendC(&cmd, " -tree");
else
if(!use_dend)
ajStrAppendC(&cmd, " -align");
/* Set sequence type from information from acd file */
if(are_prot)
ajStrAppendC(&cmd, " -type=protein");
else
ajStrAppendC(&cmd, " -type=dna");
/*
** set output to MSF format - will read in this file later and output
** user requested format
*/
ajStrAppendC(&cmd, " -output=");
ajStrAppendC(&cmd, "gcg");
/* If going to do pairwise alignment */
if(!use_dend)
{
/* add fast pairwise alignments*/
if(!do_slow)
{
ajStrAppendC(&cmd, " -quicktree");
ajStrAppendC(&cmd, " -ktuple=");
ajStrFromInt(&tmp, ktup);
ajStrAppendS(&cmd, tmp);
ajStrAppendC(&cmd, " -window=");
ajStrFromInt(&tmp, window);
ajStrAppendS(&cmd, tmp);
if(nopercent)
ajStrAppendC(&cmd, " -score=percent");
else
ajStrAppendC(&cmd, " -score=absolute");
ajStrAppendC(&cmd, " -topdiags=");
ajStrFromInt(&tmp, topdiags);
ajStrAppendS(&cmd, tmp);
ajStrAppendC(&cmd, " -pairgap=");
ajStrFromInt(&tmp, gapw);
ajStrAppendS(&cmd, tmp);
}
else
{
if(pairwise_matrix)
{
if(are_prot)
ajStrAppendC(&cmd, " -pwmatrix=");
else
ajStrAppendC(&cmd, " -pwdnamatrix=");
ajStrAppendS(&cmd, ajFileGetPrintnameS(pairwise_matrix));
}
else
{
if(are_prot)
{
ajStrAppendC(&cmd, " -pwmatrix=");
ajStrAppendS(&cmd, pwmstr);
}
else
{
ajStrAppendC(&cmd, " -pwdnamatrix=");
ajStrAppendS(&cmd, pwdstr);
}
}
ajStrAppendC(&cmd, " -pwgapopen=");
ajStrFromFloat(&tmp, pw_gapc, 3);
ajStrAppendS(&cmd, tmp);
ajStrAppendC(&cmd, " -pwgapext=");
ajStrFromFloat(&tmp, pw_gapv, 3);
ajStrAppendS(&cmd, tmp);
}
}
/* Multiple alignments */
/* using existing tree or generating new tree? */
if(use_dend)
{
ajStrAppendC(&cmd, " -usetree=");
ajStrAppendS(&cmd, dend_filename);
}
else
{
/* use tmp file to hold dend file, will read back in later */
tmp_dendfilename = emma_getUniqueFileName();
ajStrAppendC(&cmd, " -newtree=");
ajStrAppendS(&cmd, tmp_dendfilename);
}
if(ma_matrix)
{
if(are_prot)
ajStrAppendC(&cmd, " -matrix=");
else
ajStrAppendC(&cmd, " -pwmatrix=");
ajStrAppendS(&cmd, ajFileGetPrintnameS(ma_matrix));
}
else
{
if(are_prot)
{
ajStrAppendC(&cmd, " -matrix=");
ajStrAppendS(&cmd, m1str);
}
else
{
ajStrAppendC(&cmd, " -dnamatrix=");
ajStrAppendS(&cmd, m2str);
}
}
ajStrAppendC(&cmd, " -gapopen=");
ajStrFromFloat(&tmp, gapc, 3);
ajStrAppendS(&cmd, tmp);
ajStrAppendC(&cmd, " -gapext=");
ajStrFromFloat(&tmp, gapv, 3);
ajStrAppendS(&cmd, tmp);
ajStrAppendC(&cmd, " -gapdist=");
ajStrFromInt(&tmp, gap_dist);
ajStrAppendS(&cmd, tmp);
ajStrAppendC(&cmd, " -hgapresidues=");
ajStrAppendS(&cmd, hgapres);
if(!endgaps)
ajStrAppendC(&cmd, " -endgaps");
if(norgap)
ajStrAppendC(&cmd, " -nopgap");
if(nohgap)
ajStrAppendC(&cmd, " -nohgap");
ajStrAppendC(&cmd, " -maxdiv=");
ajStrFromInt(&tmp, maxdiv);
ajStrAppendS(&cmd, tmp);
/* run clustalw */
/* ajFmtError("..%s..\n\n", ajStrGetPtr( cmd)); */
ajDebug("Executing '%S'\n", cmd);
ajSysExecS(cmd);
/* produce alignment file only if one was produced */
if(!only_dend)
{
/* read in tmp alignment output file to output through EMBOSS output */
seqin = ajSeqinNew();
/*
** add the Usa format to the start of the filename to tell EMBOSS
** format of file
*/
ajStrInsertC(&tmp_aln_outfile, 0, "msf::");
ajSeqinUsa(&seqin, tmp_aln_outfile);
seqset = ajSeqsetNew();
if(ajSeqsetRead(seqset, seqin))
{
ajSeqoutWriteSet(seqout, seqset);
ajSeqoutClose(seqout);
ajSeqinDel(&seqin);
/* remove the Usa from the start of the string */
ajStrCutStart(&tmp_aln_outfile, 5);
}
else
ajFmtError("Problem writing out EMBOSS alignment file\n");
}
/* read in new tmp dend file (if produced) to output through EMBOSS */
if(tmp_dendfilename!=NULL)
{
tmp_dendfile = ajFileNewInNameS( tmp_dendfilename);
if(tmp_dendfile!=NULL){
while(ajReadlineTrim(tmp_dendfile, &line))
ajFmtPrintF(dend_outfile, "%s\n", ajStrGetPtr( line));
ajFileClose(&tmp_dendfile);
ajSysFileUnlinkS(tmp_dendfilename);
}
}
ajSysFileUnlinkS(tmpFilename);
if(!only_dend)
ajSysFileUnlinkS(tmp_aln_outfile);
ajStrDel(&pw_matrix);
ajStrDel(&matrix);
ajStrDel(&pw_dna_matrix);
ajStrDel(&dna_matrix);
ajStrDel(&tmp_dendfilename);
ajStrDel(&dend_filename);
ajStrDel(&tmp_aln_outfile);
ajStrDel(&pwmstr);
ajStrDel(&pwdstr);
ajStrDel(&m1str);
ajStrDel(&m2str);
ajStrDel(&hgapres);
ajStrDel(&cmd);
ajStrDel(&tmp);
ajStrDel(&tmpFilename);
ajStrDel(&line);
ajFileClose(&dend_outfile);
ajFileClose(&tmp_dendfile);
ajFileClose(&dend_file);
ajFileClose(&pairwise_matrix);
ajFileClose(&ma_matrix);
ajSeqallDel(&seqall);
ajSeqsetDel(&seqset);
ajSeqDel(&seq);
ajSeqoutDel(&seqout);
ajSeqoutDel(&fil_file);
ajSeqinDel(&seqin);
embExit();
return 0;
}
int main(int argc, char **argv)
{
ajint famn = 0; /* Counter for the families. */
ajint nset = 0; /* No. entries in family. */
ajint last_nodeid = 0; /* SCOP Sunid of last family that was
processed. */
AjPStr last_node = NULL; /* Last family that was processed. */
AjPStr exec = NULL; /* The UNIX command line to be executed. */
AjPStr out = NULL; /* Name of stamp alignment file. */
AjPStr align = NULL; /* Name of sequence alignment file. */
AjPStr alignc = NULL; /* Name of structure alignment file. */
AjPStr log = NULL; /* Name of STAMP log file. */
AjPStr dom = NULL; /* Name of file containing single domain. */
AjPStr set = NULL; /* Name of file containing set of domains. */
AjPStr scan = NULL; /* Name of temp. file used by STAMP. */
AjPStr sort = NULL; /* Name of temp. file used by STAMP. */
AjPStr name = NULL; /* Base name of STAMP temp files. */
AjPStr pdbnames = NULL; /* Names of domain pdb files to be passed to
TCOFFEEE. */
AjPDir pdb = NULL; /* Path of domain coordinate files (pdb
format input). */
AjPDirout daf = NULL; /* Path of sequence alignment files for output. */
AjPDirout super = NULL; /* Path of structure alignment files for output. */
AjPDirout singlets = NULL; /* Path of FASTA singlet sequence files for output. */
AjPStr temp1 = NULL; /* A temporary string. */
AjPFile dcfin = NULL; /* File pointer for original Escop.dat file.*/
AjPFile domf = NULL; /* File pointer for single domain file. */
AjPFile setf = NULL; /* File pointer for domain set file. */
AjPFile logf = NULL; /* Log file. */
AjPDomain domain = NULL; /* Pointer to domain structure. */
AjPDomain prevdomain = NULL; /* Pointer to previous domain structure. */
ajint type = 0; /* Type of domain (ajSCOP or ajCATH) in the
DCF file. */
AjPStr *node = NULL; /* Node of alignment . */
ajint noden = 0; /*1: Class (SCOP), 2: Fold (SCOP) etc, see
ACD file. */
AjPStr *mode = NULL; /* Mode of operation from acd*/
ajint moden = 0; /* Program mode, 1: MODE_STAMP, 2: MODE_TCOFFEE (not
yet implemented). */
AjBool keepsinglets= ajFalse; /*Whether to retain sequences of singlet families
and write them to an output file. */
AjPStr temp = NULL; /* A temporary string. */
AjPStr cmd = NULL; /* The command line to execute t-coffee. */
/* Initialise strings etc*/
last_node = ajStrNew();
exec = ajStrNew();
out = ajStrNew();
align = ajStrNew();
alignc = ajStrNew();
log = ajStrNew();
dom = ajStrNew();
set = ajStrNew();
scan = ajStrNew();
sort = ajStrNew();
name = ajStrNew();
temp = ajStrNew();
temp1 = ajStrNew();
cmd = ajStrNew();
pdbnames = ajStrNew();
/* Read data from acd. */
embInitPV("domainalign",argc,argv,"DOMALIGN",VERSION);
dcfin = ajAcdGetInfile("dcfinfile");
pdb = ajAcdGetDirectory("pdbdir");
daf = ajAcdGetOutdir("dafoutdir");
super = ajAcdGetOutdir("superoutdir");
singlets = ajAcdGetOutdir("singletsoutdir");
node = ajAcdGetList("node");
mode = ajAcdGetList("mode");
keepsinglets = ajAcdGetToggle("keepsinglets");
logf = ajAcdGetOutfile("logfile");
/* Convert the selected node and mode to an integer. */
if(!(ajStrToInt(node[0], &noden)))
ajFatal("Could not parse ACD node option");
if(!(ajStrToInt(mode[0], &moden)))
ajFatal("Could not parse ACD node option");
/* Initialise random number generator for naming of temp. files. */
ajRandomSeed();
ajFilenameSetTempname(&name);
/* Create names for temp. files. */
ajStrAssignS(&log, name);
ajStrAppendC(&log, ".log");
ajStrAssignS(&dom, name);
ajStrAppendC(&dom, ".dom");
ajStrAssignS(&set, name);
ajStrAppendC(&set, ".set");
ajStrAssignS(&scan, name);
ajStrAppendC(&scan, ".scan");
ajStrAssignS(&sort, name);
ajStrAppendC(&sort, ".sort");
ajStrAssignS(&out, name);
ajStrAppendC(&out, ".out");
/* Initialise last_node with something that is not in SCOP. */
ajStrAssignC(&last_node,"!!!!!");
/* Open STAMP domain set file. */
if(moden == MODE_STAMP)
{
if(!(setf=ajFileNewOutNameS(set)))
ajFatal("Could not open domain set file\n");
}
/* Get domain type. */
type = ajDomainDCFType(dcfin);
/* Start of main application loop. */
while((domain=(ajDomainReadCNew(dcfin, "*", type))))
{
/* A new family. */
if(((domain->Type == ajSCOP) &&
(((noden==1) && (last_nodeid != domain->Scop->Sunid_Class)) ||
((noden==2) && (last_nodeid != domain->Scop->Sunid_Fold)) ||
((noden==3) && (last_nodeid != domain->Scop->Sunid_Superfamily))||
((noden==4) && (last_nodeid != domain->Scop->Sunid_Family)))) ||
((domain->Type == ajCATH) &&
(((noden==5) && (last_nodeid != domain->Cath->Class_Id)) ||
((noden==6) && (last_nodeid != domain->Cath->Arch_Id)) ||
((noden==7) && (last_nodeid != domain->Cath->Topology_Id)) ||
((noden==8) && (last_nodeid != domain->Cath->Superfamily_Id)) ||
((noden==9) && (last_nodeid != domain->Cath->Family_Id)))))
{
/* If we have done the first family. */
if(famn)
{
/* Create the output file for the alignment - the name will
be the same as the Sunid for the DOMAIN family. */
domainalign_writeid(prevdomain, noden, daf, super,
&align, &alignc);
if(moden == MODE_STAMP)
{
/* Close domain set file. */
ajFileClose(&setf);
/* Call STAMP. */
/* Family with 2 or more entries. */
if(nset > 1)
{
domainalign_stamp(prevdomain,
domain,
daf,
super,
singlets,
align,
alignc,
dom,
name,
set,
scan,
sort,
log,
out,
keepsinglets,
moden,
noden,
nset,
logf);
}
else if(keepsinglets) /* Singlet family. */
domainalign_keepsinglets(prevdomain, noden,
singlets, logf);
/* Open STAMP domain set file. */
if(!(setf=ajFileNewOutNameS(set)))
ajFatal("Could not open domain set file\n");
}
else
{
/* Call TCOFEE. */
if(nset > 1)
domainalign_tcoffee(prevdomain, out, align,
alignc, pdbnames, noden, logf);
else if(keepsinglets) /* Singlet family. */
domainalign_keepsinglets(prevdomain, noden,
singlets, logf);
}
/* Set the number of members of the new family to zero. */
nset = 0;
/* Clear TCOFFEE argument. */
ajStrSetClear(&pdbnames);
}
/* Open, write and close STAMP domain file. */
if(moden == MODE_STAMP)
{
if(!(domf=ajFileNewOutNameS(dom)))
ajFatal("Could not open domain file\n");
ajStrAssignS(&temp, ajDomainGetId(domain));
ajStrFmtLower(&temp);
ajFmtPrintF(domf, "%S %S { ALL }\n", temp, temp);
ajFileClose(&domf);
}
/* Copy current family name to last_node. */
domainalign_writelast(domain, noden, &last_node, &last_nodeid);
/* Copy current domain pointer to prevdomain. */
ajDomainDel(&prevdomain);
prevdomain=NULL;
ajDomainCopy(&prevdomain, domain);
/* Increment family counter. */
famn++;
}
ajStrAssignS(&temp, ajDomainGetId(domain));
ajStrFmtLower(&temp);
/* Write STAMP domain set file. */
if(moden == MODE_STAMP)
ajFmtPrintF(setf, "%S %S { ALL }\n", temp, temp);
/* Write TCOFFEE argument. */
else
{
ajStrAppendS(&pdbnames, ajDirGetPath(pdb));
ajStrAppendS(&pdbnames, temp);
ajStrAppendC(&pdbnames, ".");
ajStrAppendS(&pdbnames, ajDirGetExt(pdb));
ajStrAppendC(&pdbnames, " ");
}
ajDomainDel(&domain);
/* Increment number of members in family. */
nset++;
}
/* End of main application loop. */
domain=prevdomain;
ajFmtPrint("\nProcessing node %d\n", last_nodeid);
/* Create the output file for the alignment - the name will
be the same as the Sunid for the DOMAIN family. */
domainalign_writeid(prevdomain, noden, daf, super, &align, &alignc);
/* Code to process last family. */
if(moden == MODE_STAMP)
{
/*Close domain set file. */
ajFileClose(&setf);
/* ajFmtPrint("\n***** SECOND CALL\n");. */
if(nset > 1)
{
domainalign_stamp(prevdomain,
domain,
daf,
super,
singlets,
align,
alignc,
dom,
name,
set,
scan,
sort,
log,
out,
keepsinglets,
moden,
noden,
nset,
logf);
}
else if(keepsinglets) /* Singlet family. */
domainalign_keepsinglets(prevdomain, noden, singlets, logf);
}
else
{
/* Call TCOFEE. */
if(nset > 1)
domainalign_tcoffee(prevdomain, out, align, alignc,
pdbnames, noden, logf);
else if(keepsinglets) /* Singlet family. */
domainalign_keepsinglets(prevdomain, noden, singlets, logf);
}
/* Remove all temporary files. */
ajSysFileUnlinkS(log);
ajSysFileUnlinkS(dom);
ajSysFileUnlinkS(set);
ajSysFileUnlinkS(scan);
ajSysFileUnlinkS(sort);
ajSysFileUnlinkS(out);
ajStrAssignS(&temp, name);
ajStrAppendC(&temp, ".mat");
ajSysFileUnlinkS(temp);
/* Tidy up*/
ajDomainDel(&domain);
ajFileClose(&dcfin);
ajStrDel(&last_node);
ajStrDel(&exec);
ajStrDel(&log);
ajStrDel(&dom);
ajStrDel(&set);
ajStrDel(&scan);
ajStrDel(&sort);
ajStrDel(&name);
ajStrDel(&out);
ajStrDel(&align);
ajStrDel(&alignc);
ajStrDel(&pdbnames);
ajDirDel(&pdb);
ajDiroutDel(&daf);
ajDiroutDel(&super);
ajDiroutDel(&singlets);
ajStrDel(&temp);
ajStrDel(&temp1);
ajStrDel(&node[0]);
AJFREE(node);
ajStrDel(&mode[0]);
AJFREE(mode);
ajFileClose(&logf);
ajExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gdeltagcskew", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjBool at = 0;
AjBool purine = 0;
AjBool keto = 0;
AjPStr method = 0;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjPFilebuff tmp = NULL;
AjPStr line = NULL;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
at = ajAcdGetBoolean("at");
purine = ajAcdGetBoolean("purine");
keto = ajAcdGetBoolean("keto");
method = ajAcdGetSelectSingle("method");
accid = ajAcdGetBoolean("accid");
outf = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajDie("Output file (%S) open error\n", tmpname);
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajWarn("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
if(accid)
{
ajStrAssignS(&restid, seqid);
if(ajStrGetLen(seqid) == 0)
{
ajDie("Cannot proceed without header with -accid\n");
}
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/delta_gcskew/", base, restid);
if(!gFilebuffURLS(url, &tmp))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajBuffreadLine(tmp, &line);
ajStrRemoveSetC(&line, "\n");
ajFmtPrintF(outf, "Sequence: %S DELTA-GCskew %S\n", seqid, line);
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gldabias", argc, argv, "GEMBASSY", "1.0.1");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
ajint coefficients = 0;
AjPStr variable = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjPFilebuff tmp = NULL;
AjPStr line = NULL;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
coefficients = ajAcdGetInt("coefficients");
variable = ajAcdGetSelectSingle("variable");
accid = ajAcdGetBoolean("accid");
outf = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajDie("Output file (%S) open error\n", tmpname);
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajDie("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
if(accid)
{
ajStrAssignS(&restid, ajSeqGetAccS(seq));
if(!ajStrGetLen(restid))
{
ajStrAssignS(&restid, ajSeqGetNameS(seq));
}
if(!ajStrGetLen(restid))
{
ajDie("No valid header information\n");
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/lda_bias/coefficients=%d/variable=%S",
base, restid, coefficients, variable);
if(!gFilebuffURLS(url, &tmp))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajBuffreadLine(tmp, &line);
ajStrRemoveSetC(&line, "\n");
ajFmtPrintF(outf, "Sequence: %S LDA-BIAS: %S\n", seqid, line);
ajStrDel(&url);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("ggcskew", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPStr tmpname = NULL;
AjPSeqout tmpout = NULL;
ajint window = 0;
ajint slide = 0;
AjBool cumulative = 0;
AjBool at = 0;
AjBool purine = 0;
AjBool keto = 0;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
seqall = ajAcdGetSeqall("sequence");
window = ajAcdGetInt("window");
slide = ajAcdGetInt("slide");
cumulative = ajAcdGetBoolean("cumulative");
at = ajAcdGetBoolean("at");
purine = ajAcdGetBoolean("purine");
keto = ajAcdGetBoolean("keto");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
ajStrAppendC(&tmpname, ".fasta");
while(ajSeqallNext(seqall, &seq))
{
tmpout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(tmpout, tmpname))
{
embExitBad();
}
ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
ajSeqoutWriteSeq(tmpout, seq);
ajSeqoutClose(tmpout);
ajSeqoutDel(&tmpout);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/gcskew/window=%d/slide=%d/cumulative=%d/"
"at=%d/purine=%d/keto=%d/output=f/", base, restid, window,
slide, cumulative, at, purine, keto);
if(plot)
{
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("location");
gpp.ylab = ajStrNewC("GC skew");
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("genret", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq = NULL;
AjPStr inseq = NULL;
AjPStr gene = NULL;
AjPStr access = NULL;
AjBool accid = ajTrue;
AjPStr argument = NULL;
AjPFile outfile = NULL;
AjPStr seqid = NULL;
AjPStr restid = NULL;
AjBool valid = ajFalse;
AjBool isseq = ajFalse;
AjBool isgbk = ajFalse;
AjPFilebuff buff = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjPStr regexstr = NULL;
AjPStrTok token = NULL;
AjPRegexp regex = NULL;
AjPStr url = NULL;
AjPStr base = NULL;
AjPStr head = NULL;
AjPStr line = NULL;
seqall = ajAcdGetSeqall("sequence");
access = ajAcdGetString("access");
gene = ajAcdGetString("gene");
argument = ajAcdGetString("argument");
accid = ajAcdGetBoolean("accid");
outfile = ajAcdGetOutfile("outfile");
if(
ajStrMatchC(access, "translation") ||
ajStrMatchC(access, "get_exon") ||
ajStrMatchC(access, "get_exons") ||
ajStrMatchC(access, "get_cdsseq") ||
ajStrMatchC(access, "get_gbkseq") ||
ajStrMatchC(access, "get_geneseq") ||
ajStrMatchC(access, "get_intron") ||
ajStrMatchC(access, "getseq") ||
ajStrMatchC(access, "seq") ||
ajStrMatchC(access, "around_startcodon") ||
ajStrMatchC(access, "around_stopcodon") ||
ajStrMatchC(access, "before_startcodon") ||
ajStrMatchC(access, "before_stopcodon") ||
ajStrMatchC(access, "after_startcodon") ||
ajStrMatchC(access, "after_stopcodon")
)
{
isseq = ajTrue;
}
else if(ajStrMatchC(access, "annotate") ||
ajStrMatchC(access, "output"))
{
isgbk = ajTrue;
}
else
{
ajFmtPrintF(outfile, "gene,%S\n", access);
}
base = ajStrNewC("rest.g-language.org");
ajStrExchangeCC(&argument, " ", "/");
ajStrExchangeCC(&argument, ",", "/");
ajStrExchangeCC(&argument, "\t", "/");
ajStrExchangeCC(&argument, "\r", "/");
ajStrExchangeCC(&argument, "\n", "/");
if(ajStrMatchC(gene, "*"))
{
ajStrInsertK(&gene, 0, '.');
}
if(ajStrPrefixC(gene, "@") || ajStrPrefixC(gene, "list::"))
{
ajStrExchangeCC(&gene, "@", "");
ajStrExchangeCC(&gene, "list::", "");
ajStrAssignS(&tmpname, gene);
tmpfile = ajFileNewInNameS(tmpname);
if(!tmpfile)
{
ajDie("List file (%S) open error\n", tmpname);
}
gene = ajStrNew();
while(ajReadline(tmpfile, &line))
{
ajStrAppendS(&gene, line);
}
ajFileClose(&tmpfile);
ajStrDel(&tmpname);
ajStrDel(&line);
}
tmpname = ajStrNew();
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = ajStrNew();
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajDie("Output file (%S) open error\n", tmpname);
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajWarn("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
if(accid)
{
ajStrAssignS(&restid, seqid);
if(ajStrGetLen(seqid) == 0)
{
ajDie("Cannot proceed without header with -accid\n");
}
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
}
url = ajStrNew();
if(isgbk)
{
ajFmtPrintS(&url, "http://%S/%S/%S", base, restid, access);
}
else
{
ajFmtPrintS(&url, "http://%S/%S/*/%S/%S", base, restid, access, argument);
}
if(!gFilebuffURLS(url, &buff))
{
ajDie("GET error from %S\n", url);
}
while(ajBuffreadLine(buff, &line))
{
if(isgbk){
ajFmtPrintF(outfile, "%S", line);
continue;
}
ajStrRemoveLastNewline(&line);
regex = ajRegCompC("^>");
if(ajRegExec(regex, line))
{
head = ajStrNew();
ajStrAssignS(&head, line);
ajStrTrimStartC(&head, ">");
valid = ajFalse;
token = ajStrTokenNewC(ajStrNewS(gene), " ,\t\r\n");
while(ajStrTokenNextParse(token, ®exstr))
{
if(ajStrGetLen(regexstr))
{
regex = ajRegComp(regexstr);
if(ajRegExec(regex, line))
{
valid = ajTrue;
if(ajStrIsAlnum(regexstr))
{
ajStrExchangeSC(&gene, regexstr, "");
}
}
ajRegFree(®ex);
}
}
}
else
{
if(valid)
{
if(isseq)
{
ajStrFmtWrap(&line, 60);
ajFmtPrintF(outfile, ">%S\n%S\n", head, line);
}
else
{
ajFmtPrintF(outfile, "%S,%S\n", head, line);
}
valid = ajFalse;
}
}
}
ajFileClose(&outfile);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&access);
ajStrDel(&gene);
embExit();
}
int main(int argc, char *argv[])
{
embInitPV("gbaseinformationcontent", argc, argv, "GEMBASSY", "1.0.1");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr position = 0;
ajint PatLen = 0;
ajint upstream = 0;
ajint downstream = 0;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjBool plot = 0;
AjPFile outf = NULL;
AjPFilebuff buff = NULL;
AjPGraph mult = NULL;
gPlotParams gpp;
AjPStr title = NULL;
seqall = ajAcdGetSeqall("sequence");
position = ajAcdGetSelectSingle("position");
PatLen = ajAcdGetInt("patlen");
upstream = ajAcdGetInt("upstream");
downstream = ajAcdGetInt("downstream");
accid = ajAcdGetBoolean("accid");
plot = ajAcdGetToggle("plot");
outf = ajAcdGetOutfile("outfile");
mult = ajAcdGetGraphxy("graph");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
gAssignUniqueName(&tmpname);
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajFmtError("Output file (%S) open error\n", tmpname);
embExitBad();
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajFmtError("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
if(accid)
{
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(!ajStrGetLen(seqid))
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(!ajStrGetLen(seqid))
{
ajFmtError("No valid header information\n");
embExitBad();
}
ajStrAssignS(&restid, seqid);
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/base_information_content/position=%S/"
"PatLen=%d/upstream=%d/downstream=%d/output=f/tag=gene",
base, restid, position, PatLen, upstream, downstream);
if(plot)
{
title = ajStrNew();
ajStrAppendC(&title, argv[0]);
ajStrAppendC(&title, " of ");
ajStrAppendS(&title, seqid);
gpp.title = ajStrNewS(title);
gpp.xlab = ajStrNewC("position");
gpp.ylab = ajStrNewC("information content");
if(!gFilebuffURLS(url, &buff))
{
ajDie("File downloading error from:\n%S\n", url);
}
if(!gPlotFilebuff(buff, mult, &gpp))
{
ajDie("Error in plotting\n");
}
AJFREE(gpp.title);
AJFREE(gpp.xlab);
AJFREE(gpp.ylab);
ajStrDel(&title);
ajFilebuffDel(&buff);
}
else
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("File downloading error from:\n%S\n", url);
}
}
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
ajStrDel(&position);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gbasezvalue", argc, argv, "GEMBASSY", "1.0.3");
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr position = NULL;
ajint limit = 0;
ajint PatLen = 0;
ajint upstream = 0;
ajint downstream = 0;
AjBool accid = ajFalse;
AjPStr restid = NULL;
AjPStr seqid = NULL;
AjPStr base = NULL;
AjPStr url = NULL;
AjPFile tmpfile = NULL;
AjPStr tmpname = NULL;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
position = ajAcdGetSelectSingle("position");
limit = ajAcdGetInt("limit");
PatLen = ajAcdGetInt("patlen");
upstream = ajAcdGetInt("upstream");
downstream = ajAcdGetInt("downstream");
accid = ajAcdGetBoolean("accid");
outf = ajAcdGetOutfile("outfile");
base = ajStrNewC("rest.g-language.org");
gAssignUniqueName(&tmpname);
while(ajSeqallNext(seqall, &seq))
{
inseq = NULL;
if(!accid)
{
if(gFormatGenbank(seq, &inseq))
{
tmpfile = ajFileNewOutNameS(tmpname);
if(!tmpfile)
{
ajDie("Output file (%S) open error\n", tmpname);
}
ajFmtPrintF(tmpfile, "%S", inseq);
ajFileClose(&tmpfile);
ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
gFilePostSS(url, tmpname, &restid);
ajStrDel(&url);
ajSysFileUnlinkS(tmpname);
}
else
{
ajWarn("Sequence does not have features\n"
"Proceeding with sequence accession ID\n");
accid = ajTrue;
}
}
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(ajStrGetLen(seqid) == 0)
{
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
}
if(ajStrGetLen(seqid) == 0)
{
ajWarn("No valid header information\n");
}
if(accid)
{
ajStrAssignS(&restid, seqid);
if(ajStrGetLen(seqid) == 0)
{
ajDie("Cannot proceed without header with -accid\n");
}
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
}
url = ajStrNew();
ajFmtPrintS(&url, "http://%S/%S/base_z_value/position=%S/PatLen=%d"
"upstream=%d/downstream=%d/limit=%d/output=f/tag=gene",
base, restid, position, PatLen, upstream, downstream, limit);
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLS(url, &outf))
{
ajDie("Failed to download result from:\n%S\n", url);
}
ajStrDel(&url);
ajStrDel(&restid);
ajStrDel(&seqid);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&base);
ajStrDel(&position);
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;
}