int main(int argc, char **argv) {
// initialize EMBASSY info
embInitPV("kclique", argc, argv, "KBWS", "1.0.9");
struct soap soap;
char* jobid;
char* result;
AjPFile infile;
AjPFile outf;
AjPStr substr;
AjPStr indata = NULL;
AjPStr line = NULL;
infile = ajAcdGetInfile("infile");
outf = ajAcdGetOutfile("outfile");
while (ajReadline(infile, &line)) {
ajStrAppendS(&indata, line);
ajStrAppendC(&indata, "\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(indata);
if ( soap_call_ns1__runClique( &soap, NULL, NULL, in0, &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);
}
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);
}
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&infile);
ajFileClose(&outf);
ajStrDel(&substr);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* ACD data item variables */
AjPFile database = NULL;
/* Housekeeping variables */
AjPStr cmd = NULL;
AjPStr tmp = NULL;
/* ACD file processing */
embInitPV("ehmmindex",argc,argv,"HMMERNEW",VERSION);
database = ajAcdGetInfile("database");
/* MAIN APPLICATION CODE */
/* 1. Housekeeping */
cmd = ajStrNew();
tmp = ajStrNew();
/* 2. Build hmmindex 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("hmmindex"));
ajStrAppendC(&cmd, ajFileGetNameC(database));
/* 3. Close ACD files. */
ajFileClose(&database);
/* 4. Call hmmindex */
ajFmtPrint("\n%S\n\n", cmd);
system(ajStrGetPtr(cmd));
/* 5. Exit cleanly */
ajStrDel(&cmd);
ajStrDel(&tmp);
embExit();
return 0;
}
/* @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;
}
int main(int argc, char **argv)
{
AjPSeq seq = NULL;
AjPFile outf = NULL;
embInitPV("myseq", argc, argv, "myemboss",VERSION);
seq = ajAcdGetSeq("sequence");
outf = ajAcdGetOutfile("outfile");
ajFmtPrintF(outf, "Sequence properties\n");
ajFmtPrintF(outf, "===================\n");
ajFmtPrintF(outf, "Name: %S\n", ajSeqGetNameS(seq));
ajFmtPrintF(outf, "Usa: %S\n", ajSeqGetUsaS(seq));
ajFmtPrintF(outf, "Length: %d\n", ajSeqGetLen(seq));
ajFileClose(&outf);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPFile listf = NULL; /* File to be read - caths.list.v2.4. */
AjPFile domf = NULL; /* File to be read - domlist.v2.4. */
AjPFile namesf = NULL; /* File to be read - CAT.names.all.v2.4. */
AjPFile outf = NULL; /* Output file. */
AjPFile logf = NULL; /* Log file. */
AjPList list = NULL; /* List of CATH objects. */
AjPCath tmp = NULL; /* Temp. pointer. */
embInitPV("cathparse", argc, argv, "DOMAINATRIX",VERSION);
listf = ajAcdGetInfile("listfile");
domf = ajAcdGetInfile("domfile");
namesf = ajAcdGetInfile("namesfile");
outf = ajAcdGetOutfile("outfile");
logf = ajAcdGetOutfile("logfile");
list = ajCathReadAllRawNew(listf, domf, namesf, logf);
while(ajListPop(list, (void **) &tmp))
{
ajCathWrite(outf, tmp);
ajCathDel(&tmp);
}
/* Close CATH parsable files and output file */
ajFileClose(&listf);
ajFileClose(&domf);
ajFileClose(&namesf);
ajFileClose(&outf);
ajFileClose(&logf);
ajListFree(&list);
ajExit();
return 0;
}
int main(int argc, char *argv[])
{
embInitPV("gpalindrome", argc, argv, "GEMBASSY", "1.0.3");
struct soap soap;
struct ns1__palindromeInputParams params;
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr seqid = NULL;
ajint shortest = 0;
ajint loop = 0;
AjBool gtmatch = 0;
char *in0;
char *result;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
shortest = ajAcdGetInt("shortest");
loop = ajAcdGetInt("loop");
gtmatch = ajAcdGetBoolean("gtmatch");
outf = ajAcdGetOutfile("outfile");
params.shortest = shortest;
params.loop = loop;
params.gtmatch = gtmatch;
params.output = "f";
while(ajSeqallNext(seqall, &seq))
{
soap_init(&soap);
inseq = NULL;
ajStrAppendC(&inseq, ">");
ajStrAppendS(&inseq, ajSeqGetNameS(seq));
ajStrAppendC(&inseq, "\n");
ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
in0 = ajCharNewS(inseq);
if(soap_call_ns1__palindrome(
&soap,
NULL,
NULL,
in0,
¶ms,
&result
) == SOAP_OK)
{
ajFmtPrintF(outf, "Sequence: %S\n", seqid);
if(!gFileOutURLC(result, &outf))
{
ajDie("File downloading error from:\n%s\n", result);
embExitBad();
}
}
else
{
soap_print_fault(&soap, stderr);
}
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
AJFREE(in0);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* ACD data item variables */
AjPSeqset alignfile = NULL;
AjPFile prior = NULL;
AjPFile null = NULL;
AjPFile pam = NULL;
float pamwgt = 0.0;
AjPStr nhmm = NULL;
AjPStr strategy = NULL;
ajint pbswitch = 0;
float archpri = 0.0;
AjBool binary = ajFalse;
AjBool fast = ajFalse;
float gapmax = 0.0;
AjBool hand = ajFalse;
float idlevel = 0.0;
AjBool noeff = ajFalse;
float swentry = 0.0;
float swexit = 0.0;
AjBool verbosity = ajFalse;
AjPStr weighting = NULL;
AjPFile hmmfile = NULL;
AjPFile o = NULL;
AjPFile cfile = NULL;
/* Housekeeping variables */
AjPStr cmd = NULL;
AjPStr rnd1 = NULL;
AjPStr rnd2 = NULL;
AjPStr tmp = NULL;
AjPStr fmt = NULL;
char option;
AjBool fmtok = ajFalse;
AjPStr hmmfilename = NULL;
/* ACD file processing */
embInitPV("ehmmbuild",argc,argv,"HMMERNEW",VERSION);
alignfile = ajAcdGetSeqset("alignfile");
prior = ajAcdGetInfile("prior");
null = ajAcdGetInfile("null");
pam = ajAcdGetInfile("pam");
pamwgt = ajAcdGetFloat("pamwgt");
nhmm = ajAcdGetString("nhmm");
strategy = ajAcdGetListSingle("strategy");
pbswitch = ajAcdGetInt("pbswitch");
archpri = ajAcdGetFloat("archpri");
binary = ajAcdGetBoolean("binary");
fast = ajAcdGetBoolean("fast");
gapmax = ajAcdGetFloat("gapmax");
hand = ajAcdGetBoolean("hand");
idlevel = ajAcdGetFloat("sidlevel");
noeff = ajAcdGetBoolean("noeff");
swentry = ajAcdGetFloat("swentry");
swexit = ajAcdGetFloat("swexit");
verbosity = ajAcdGetBoolean("verbosity");
weighting = ajAcdGetListSingle("weighting");
hmmfile = ajAcdGetOutfile("hmmfile");
o = ajAcdGetOutfile("o");
cfile = ajAcdGetOutfile("cfile");
/* MAIN APPLICATION CODE */
/* 1. Housekeeping */
cmd = ajStrNew();
rnd1 = ajStrNew();
rnd2 = ajStrNew();
tmp = ajStrNew();
fmt = ajStrNew();
hmmfilename = ajStrNew();
ajStrAssignC(&hmmfilename, ajFileGetNameC(hmmfile));
/* 2. Ensure alignfile is in format HMMER can understand. These include
FASTA, GENBANK,EMBL, GCG, PIR, STOCKHOLM, SELEX, MSF,CLUSTAL and PHYLIP.
EMBOSS name definitions are taken from seqInFormatDef in ajseqread.c and
seqOutFormat in ajseqwrite.c */
fmtok=ajFalse;
ajStrAssignS(&fmt, ajSeqsetGetFormat(alignfile));
if(ajStrMatchC(fmt, "fasta") ||
ajStrMatchC(fmt, "genbank") ||
ajStrMatchC(fmt, "embl") ||
ajStrMatchC(fmt, "gcg") ||
ajStrMatchC(fmt, "pir") ||
ajStrMatchC(fmt, "stockholm")||
ajStrMatchC(fmt, "selex") ||
ajStrMatchC(fmt, "msf") ||
ajStrMatchC(fmt, "clustal") ||
ajStrMatchC(fmt, "phylip"))
fmtok = ajTrue;
/* This could be replaced with code to reformat the file. */
if(!fmtok)
ajFatal("Input alignment ('alignfile' ACD option) is not in format "
"HMMER understands. Please use a a file in FASTA, GENBANK, "
"EMBL, GCG, PIR, STOCKHOLM, SELEX, MSF,CLUSTAL or PHYLIP format.");
/* 3. Build hmmbuild 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("hmmbuild"));
if(prior)
ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior));
if(null)
ajFmtPrintS(&cmd, " --null %s ", ajFileGetNameC(null));
if(pam)
ajFmtPrintAppS(&cmd, " --pam %s --pamwgt %f ", ajFileGetNameC(pam), pamwgt);
ajFmtPrintAppS(&cmd, " -n %S ", nhmm);
/* ACD option only allows one selection */
option = ajStrGetCharFirst(strategy);
if(option == 'F')
ajStrAppendC(&cmd, " -f ");
else if(option == 'G')
ajStrAppendC(&cmd, " -g ");
else if(option == 'S')
ajStrAppendC(&cmd, " -s ");
/* else go with default ('D' option in ACD file) */
ajFmtPrintAppS(&cmd, " --pbswitch %d ", pbswitch);
ajFmtPrintAppS(&cmd, " --archpri %f ", archpri);
if(binary)
ajStrAppendC(&cmd, " --binary ");
if(fast)
ajFmtPrintAppS(&cmd, " --fast --gapmax %f ", gapmax);
if(hand)
ajStrAppendC(&cmd, " --hand ");
ajFmtPrintAppS(&cmd, " --idlevel %f ", idlevel);
if(noeff)
ajStrAppendC(&cmd, " --noeff ");
ajFmtPrintAppS(&cmd, " --swentry %f ", swentry);
ajFmtPrintAppS(&cmd, " --swexit %f ", swexit);
if(verbosity)
ajStrAppendC(&cmd, " --verbose ");
/* ACD option only allows one selection */
option = ajStrGetCharFirst(weighting);
if(option == 'B')
ajStrAppendC(&cmd, " --wblosum ");
else if(option == 'G')
ajStrAppendC(&cmd, " --wgsc ");
else if(option == 'K')
ajStrAppendC(&cmd, " --wme ");
else if(option == 'W')
ajStrAppendC(&cmd, " --wpb ");
else if(option == 'V')
ajStrAppendC(&cmd, " --wvoronoi ");
else if(option == 'N')
ajStrAppendC(&cmd, " --wnone ");
if(o)
ajFmtPrintAppS(&cmd, " -o %s ", ajFileGetNameC(o));
if(cfile)
ajFmtPrintAppS(&cmd, " --cfile %s ", ajFileGetNameC(cfile));
/* -A (append) always set but file will be wiped by EMBOSS first unless
append: "Y" is set for "hmmfile" in the ACD file. */
ajStrAppendC(&cmd, " -A -F ");
ajFmtPrintAppS(&cmd, " %S %S", hmmfilename, ajSeqsetGetFilename(alignfile));
/* 4. Close ACD files */
ajSeqsetDel(&alignfile);
ajFileClose(&prior);
ajFileClose(&null);
ajFileClose(&pam);
ajFileClose(&hmmfile);
ajFileClose(&o);
ajFileClose(&cfile);
/* 5. Call hmmbuild */
ajFmtPrint("\n%S\n", cmd);
system(ajStrGetPtr(cmd));
/* 6. Exit cleanly */
ajStrDel(&nhmm);
ajStrDel(&cmd);
ajStrDel(&rnd1);
ajStrDel(&rnd2);
ajStrDel(&tmp);
ajStrDel(&fmt);
ajStrDel(&hmmfilename);
ajStrDel(&strategy);
ajStrDel(&weighting);
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)
{
/* 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)
{
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;
}
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("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;
}
void emboss_getoptions(char *pgm, int argc, char *argv[])
{
ajint numseqs=0;
ajint numwts=0;
AjPStr method = NULL;
ancvar = false;
dollo = true;
jumble = false;
njumble = 1;
trout = true;
usertree = false;
goteof = false;
weights = false;
justwts = false;
printdata = false;
progress = true;
treeprint = true;
stepbox = false;
ancseq = false;
mulsets = false;
msets = 1;
embInitPV(pgm, argc, argv, "PHYLIPNEW",VERSION);
phylostates = ajAcdGetDiscretestates("infile");
while (phylostates[numseqs])
numseqs++;
phylotrees = ajAcdGetTree("intreefile");
if (phylotrees)
{
numtrees = 0;
while (phylotrees[numtrees])
numtrees++;
usertree = true;
}
phyloweights = ajAcdGetProperties("weights");
if (phyloweights)
{
weights = true;
numwts = ajPhyloPropGetSize(phyloweights);
}
if (numseqs > 1) {
mulsets = true;
msets = numseqs;
}
else if (numwts > 1) {
mulsets = true;
msets = numwts;
justwts = true;
}
method = ajAcdGetListSingle("method");
if(ajStrMatchC(method, "d")) dollo = true;
else dollo = false;
if(!usertree) {
njumble = ajAcdGetInt("njumble");
if(njumble >0) {
inseed = ajAcdGetInt("seed");
jumble = true;
emboss_initseed(inseed, &inseed0, seed);
}
else njumble = 1;
}
if((mulsets) && (!jumble)) {
jumble = true;
inseed = ajAcdGetInt("seed");
emboss_initseed(inseed, &inseed0, seed);
}
phyloanc = ajAcdGetProperties("ancfile");
if(phyloanc) ancvar = true;
threshold = ajAcdGetFloat("threshold");
printdata = ajAcdGetBoolean("printdata");
progress = ajAcdGetBoolean("progress");
treeprint = ajAcdGetBoolean("treeprint");
trout = ajAcdGetToggle("trout");
stepbox = ajAcdGetBoolean("stepbox");
ancseq = ajAcdGetBoolean("ancseq");
embossoutfile = ajAcdGetOutfile("outfile");
emboss_openfile(embossoutfile, &outfile, &outfilename);
if(trout) {
embossouttree = ajAcdGetOutfile("outtreefile");
emboss_openfile(embossouttree, &outtree, &outtreename);
}
printf("\nDollo and polymorphism parsimony algorithm, version %s\n\n", VERSION);
fprintf(outfile,"\nDollo and polymorphism parsimony algorithm,");
fprintf(outfile," version %s\n\n",VERSION);
} /* emboss_getoptions */
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("gcircularmap", argc, argv, "GEMBASSY", "1.0.1");
struct soap soap;
struct ns1__circular_USCOREmapInputParams params;
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr seqid = NULL;
AjBool accid = ajFalse;
AjPFile outf = NULL;
AjPStr filename = NULL;
AjPStr outfname = NULL;
AjPStr format = NULL;
ajint i;
char *in0;
char *result;
seqall = ajAcdGetSeqall("sequence");
filename = ajAcdGetString("goutfile");
accid = ajAcdGetBoolean("accid");
format = ajAcdGetString("format");
params.gmap = 0;
i = 0;
while(ajSeqallNext(seqall, &seq))
{
soap_init(&soap);
soap.send_timeout = 0;
soap.recv_timeout = 0;
inseq = NULL;
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
if(!ajStrGetLen(seqid))
ajStrAssignS(&seqid, ajSeqGetNameS(seq));
if(!ajStrGetLen(seqid))
{
ajWarn("No valid header information\n");
}
if(accid || !gFormatGenbank(seq, &inseq))
{
if(!accid)
ajWarn("Sequence does not have features\n"
"Proceeding with sequence accession ID:%S\n", seqid);
if(!gValID(seqid))
{
ajDie("Invalid accession ID:%S, exiting\n", seqid);
}
ajStrAssignS(&inseq, seqid);
}
in0 = ajCharNewS(inseq);
if(soap_call_ns1__circular_USCOREmap(
&soap,
NULL,
NULL,
in0,
¶ms,
&result
) == SOAP_OK)
{
++i;
outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
filename,
i,
format));
outf = ajFileNewOutNameS(outfname);
if(!outf)
{
ajDie("File open error\n");
}
if(!ajStrMatchC(format, "svg"))
{
if(!gHttpConvertC(result, &outf, ajStrNewC("svg"), format))
{
ajDie("File downloading error from:\n%s\n", result);
}
else
{
ajFmtPrint("Created %S\n", outfname);
}
}
else
{
if(!gHttpGetBinC(result, &outf))
{
ajDie("File downloading error from:\n%s\n", result);
}
else
{
ajFmtPrint("Created %S\n", outfname);
}
}
ajStrDel(&outfname);
}
else
{
soap_print_fault(&soap, stderr);
}
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
AJFREE(in0);
ajStrDel(&inseq);
}
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
ajStrDel(&filename);
embExit();
return 0;
}
int main(int argc, char **argv)
{
const char *hmmfile; /* file to read HMMs from */
FILE *fp; /* output file handle */
HMMFILE *hmmfp; /* opened hmmfile for reading */
struct plan7_s *hmm; /* HMM to generate from */
int L; /* length of a sequence */
int i; /* counter over sequences */
char *ofile; /* output sequence file */
int nseq; /* number of seqs to sample */
int seed; /* random number generator seed */
int be_quiet; /* TRUE to silence header/footer */
int do_alignment; /* TRUE to output in aligned format */
int do_consensus; /* TRUE to do a single consensus seq */
AjBool ajselex;
AjBool ajcons;
AjPFile inf=NULL;
AjPFile outf=NULL;
AjPStr instr=NULL;
AjPStr outstr=NULL;
#ifdef MEMDEBUG
unsigned long histid1, histid2, orig_size, current_size;
orig_size = malloc_inuse(&histid1);
fprintf(stderr, "[... memory debugging is ON ...]\n");
#endif
/***********************************************
* Parse command line
***********************************************/
nseq = 10;
be_quiet = FALSE;
do_alignment = FALSE;
do_consensus = FALSE;
ofile = NULL;
embInitPV("ohmmemit",argc,argv,"HMMER",VERSION);
ajselex = ajAcdGetBoolean("selex");
ajcons = ajAcdGetBoolean("consensus");
nseq = ajAcdGetInt("number");
seed = ajAcdGetInt("seed");
inf = ajAcdGetInfile("infile");
outf = ajAcdGetOutfile("outfile");
if(!seed)
seed = time ((time_t *) NULL);
if(ajselex)
do_alignment=TRUE;
else
do_alignment=FALSE;
if(ajcons)
do_consensus=TRUE;
else
do_consensus=FALSE;
instr = ajStrNewC((char *)ajFileGetNameC(inf));
outstr = ajStrNewC((char *)ajFileGetNameC(outf));
hmmfile = ajStrGetPtr(instr);
sre_srandom(seed);
if (do_alignment && do_consensus)
ajFatal("Sorry, -selex and -consensus are incompatible.\n");
if (nseq != 10 && do_consensus)
ajWarn("-consensus overrides -number (# of sampled seqs)");
/***********************************************
* Open HMM file (might be in HMMERDB or current directory).
* Read a single HMM from it.
***********************************************/
if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL)
ajFatal("Failed to open HMM file %s\n", hmmfile);
if (!HMMFileRead(hmmfp, &hmm))
ajFatal("Failed to read any HMMs from %s\n", hmmfile);
HMMFileClose(hmmfp);
if (hmm == NULL)
ajFatal("HMM file %s corrupt or in incorrect format? Parse failed",
hmmfile);
/* Configure the HMM to shut off N,J,C emission: so we
* do a simple single pass through the model.
*/
Plan7NakedConfig(hmm);
Plan7Renormalize(hmm);
/***********************************************
* Open the output file, or stdout
***********************************************/
fp = ajFileGetFileptr(outf);
/***********************************************
* Show the options banner
***********************************************/
be_quiet=TRUE;
if (! be_quiet)
{
printf("HMM file: %s\n", hmmfile);
if (! do_consensus)
{
printf("Number of seqs: %d\n", nseq);
printf("Random seed: %d\n", seed);
}
printf("- - - - - - - - - - - - - - - - - - - - - - - - - "
"- - - - - - -\n\n");
}
/***********************************************
* Do the work.
* If we're generating an alignment, we have to collect
* all our traces, then output. If we're generating unaligned
* sequences, we can emit one at a time.
***********************************************/
if (do_consensus)
{
char *seq;
SQINFO sqinfo; /* info about sequence (name/desc) */
EmitConsensusSequence(hmm, &seq, NULL, &L, NULL);
strcpy(sqinfo.name, "consensus");
sqinfo.len = L;
sqinfo.flags = SQINFO_NAME | SQINFO_LEN;
WriteSeq(fp, kPearson, seq, &sqinfo);
free(seq);
}
else if (do_alignment)
{
struct p7trace_s **tr;
char **dsq;
SQINFO *sqinfo;
char **aseq;
AINFO ainfo;
float *wgt;
dsq = MallocOrDie(sizeof(char *) * nseq);
tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq);
sqinfo = MallocOrDie(sizeof(SQINFO) * nseq);
wgt = MallocOrDie(sizeof(float) * nseq);
FSet(wgt, nseq, 1.0);
for (i = 0; i < nseq; i++)
{
EmitSequence(hmm, &(dsq[i]), &L, &(tr[i]));
sprintf(sqinfo[i].name, "seq%d", i+1);
sqinfo[i].len = L;
sqinfo[i].flags = SQINFO_NAME | SQINFO_LEN;
}
P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, FALSE,
&aseq, &ainfo);
/* Output the alignment */
WriteSELEX(fp, aseq, &ainfo, 50);
if (ofile != NULL && !be_quiet)
printf("Alignment saved in file %s\n", ofile);
/* Free memory
*/
for (i = 0; i < nseq; i++)
{
P7FreeTrace(tr[i]);
free(dsq[i]);
}
FreeAlignment(aseq, &ainfo);
free(sqinfo);
free(dsq);
free(wgt);
free(tr);
}
else /* unaligned sequence output */
{
struct p7trace_s *tr;
char *dsq;
char *seq;
SQINFO sqinfo;
for (i = 0; i < nseq; i++)
{
EmitSequence(hmm, &dsq, &L, &tr);
sprintf(sqinfo.name, "seq%d", i+1);
sqinfo.len = L;
sqinfo.flags = SQINFO_NAME | SQINFO_LEN;
seq = DedigitizeSequence(dsq, L);
WriteSeq(fp, kPearson, seq, &sqinfo);
P7FreeTrace(tr);
free(dsq);
free(seq);
}
}
ajFileClose(&outf);
FreePlan7(hmm);
SqdClean();
#ifdef MEMDEBUG
current_size = malloc_inuse(&histid2);
if (current_size != orig_size)
malloc_list(2, histid1, histid2);
else
fprintf(stderr, "[No memory leaks.]\n");
#endif
ajStrDel(&instr);
ajStrDel(&outstr);
ajFileClose(&inf);
ajFileClose(&outf);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqset seqset = NULL;
AjPStr cl = NULL;
AjPSeqout seqout = NULL;
float cutoff = 0.;
AjBool best = ajFalse;
AjBool gff = ajFalse;
AjBool two = ajFalse;
AjBool kinase = ajFalse;
AjPStr rsd = NULL;
AjBool addseq = ajFalse;
AjBool plot = ajFalse;
const AjPStr ofn = NULL;
AjPStr fn = NULL;
AjPStr stmp = NULL;
AjPFile outf = NULL;
embInitPV("enetphos", argc, argv, "CBSTOOLS", VERSION);
seqset = ajAcdGetSeqset("sequence");
outf = ajAcdGetOutfile("outfile");
plot = ajAcdGetBoolean("plot");
best = ajAcdGetBoolean("best");
gff = ajAcdGetBoolean("gff");
two = ajAcdGetBoolean("two");
kinase = ajAcdGetBoolean("kinase");
addseq = ajAcdGetBoolean("addseq");
cutoff = ajAcdGetFloat("cutoff");
rsd = ajAcdGetListSingle("residue");
cl = ajStrNewC("netphos ");
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(rsd,"serine"))
ajStrAppendC(&cl," -s");
else if(ajStrMatchC(rsd,"threonine"))
ajStrAppendC(&cl," -t");
else if(ajStrMatchC(rsd,"tyrosine"))
ajStrAppendC(&cl," -y");
if(plot)
ajStrAppendC(&cl," -g");
if(two)
ajStrAppendC(&cl," -2");
if(best)
ajStrAppendC(&cl," -b");
if(gff)
ajStrAppendC(&cl," -f gff");
if(kinase)
ajStrAppendC(&cl," -k");
if(addseq)
ajStrAppendC(&cl," -S");
ajFmtPrintS(&stmp," -c %f",cutoff);
ajStrAppendS(&cl,stmp);
ajFmtPrintS(&stmp," %S",fn);
ajStrAppendS(&cl,stmp);
ofn = ajFileGetNameS(outf);
ajFmtPrintS(&stmp," > %S",ofn);
ajStrAppendS(&cl,stmp);
ajFileClose(&outf);
#if 0
ajFmtPrint("%S\n",cl);
#endif
#if 1
if(system(ajStrGetPtr(cl)) == -1)
ajFatal("Command %S failed",cl);
#endif
ajSysFileUnlink(fn);
ajStrDel(&cl);
ajStrDel(&fn);
ajStrDel(&stmp);
ajStrDel(&rsd);
ajSeqoutDel(&seqout);
ajSeqsetDel(&seqset);
embExit();
return 0;
}
int main(int argc, char *argv[])
{
char *string/*, *line*/;
char *structure=NULL, *cstruc=NULL;
/*char fname[13], ffname[20], gfname[20];*/
/*char *ParamFile=NULL;*/
char *ns_bases=NULL, *c;
int i, length, l, sym/*, r*/;
double energy, min_en;
double kT, sfact=1.07;
int pf=0, noPS=0, istty;
int noconv=0;
int circ=0;
AjPSeq seq = NULL;
AjPFile confile = NULL;
AjPFile paramfile = NULL;
AjPFile outf = NULL;
AjPFile essfile = NULL;
AjPFile dotfilea = NULL;
AjPFile dotfileb = NULL;
AjPStr seqstring = NULL;
AjPStr constring = NULL;
AjPStr seqname = NULL;
float eT = 0.;
AjBool eGU;
AjBool ecirc = ajFalse;
AjBool eclose;
AjBool lonely;
AjBool convert;
AjPStr ensbases = NULL;
AjBool etloop;
AjPStr eenergy = NULL;
char ewt = '\0';
float escale = 0.;
AjPStr edangles = NULL;
char edangle = '\0';
ajint len;
embInitPV("vrnafold",argc,argv,"VIENNA",VERSION);
seqstring = ajStrNew();
constring = ajStrNew();
seqname = ajStrNew();
seq = ajAcdGetSeq("sequence");
confile = ajAcdGetInfile("constraintfile");
paramfile = ajAcdGetInfile("paramfile");
eT = ajAcdGetFloat("temperature");
ecirc = ajAcdGetBoolean("circular");
eGU = ajAcdGetBoolean("gu");
eclose = ajAcdGetBoolean("closegu");
lonely = ajAcdGetBoolean("lp");
convert = ajAcdGetBoolean("convert");
ensbases = ajAcdGetString("nsbases");
etloop = ajAcdGetBoolean("tetraloop");
eenergy = ajAcdGetListSingle("energy");
escale = ajAcdGetFloat("scale");
edangles = ajAcdGetListSingle("dangles");
outf = ajAcdGetOutfile("outfile");
essfile = ajAcdGetOutfile("ssoutfile");
/*
dotfilea = ajAcdGetOutfile("adotoutfile");
dotfileb = ajAcdGetOutfile("bdotoutfile");
*/
do_backtrack = 2;
pf = 0;
string = NULL;
istty = 0;
temperature = (double) eT;
circ = !!ecirc;
noGU = (eGU) ? 0 : 1;
no_closingGU = (eclose) ? 0 : 1;
noLonelyPairs = (lonely) ? 0 : 1;
noconv = (convert) ? 0 : 1;
ns_bases = (ajStrGetLen(ensbases)) ? MAJSTRGETPTR(ensbases) : NULL;
tetra_loop = !!etloop;
ewt = *ajStrGetPtr(eenergy);
if(ewt == '0')
energy_set = 0;
else if(ewt == '1')
energy_set = 1;
else if(ewt == '2')
energy_set = 2;
sfact = (double) escale;
edangle = *ajStrGetPtr(edangles);
if(edangle == '0')
dangles = 0;
else if(edangle == '1')
dangles = 1;
else if(edangle == '2')
dangles = 2;
else if(edangle == '3')
dangles = 3;
if(circ && noLonelyPairs)
{
ajWarn("Depending on the origin of the circular sequence\n"
"some structures may be missed when using -noLP\nTry "
"rotating your sequence a few times\n");
}
if(paramfile)
read_parameter_file(paramfile);
if (ns_bases != NULL)
{
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-')
{
sym=1; c++;
}
while (*c!='\0')
{
if (*c!=',')
{
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1)))
{
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
if(confile)
vienna_GetConstraints(confile,&constring);
string = NULL;
structure = NULL;
length = ajSeqGetLen(seq);
string = (char *) space(length+1);
strcpy(string,ajSeqGetSeqC(seq));
len = ajStrGetLen(constring);
structure = (char *) space(length+1);
if(len)
{
fold_constrained = 1;
strcpy(structure,ajStrGetPtr(constring));
}
for (l = 0; l < length; l++) {
string[l] = toupper(string[l]);
if (!noconv && string[l] == 'T') string[l] = 'U';
}
/* initialize_fold(length); */
if (circ)
min_en = circfold(string, structure);
else
min_en = fold(string, structure);
ajFmtPrintF(outf,"%s\n%s", string, structure);
if (istty)
printf("\n minimum free energy = %6.2f kcal/mol\n", min_en);
else
ajFmtPrintF(outf," (%6.2f)\n", min_en);
if (!noPS)
{
if (length<2000)
(void) PS_rna_plot(string, structure, essfile);
else
ajWarn("Structure too long, not doing xy_plot\n");
}
if (length>=2000) free_arrays();
if (pf)
{
char *pf_struc;
pf_struc = (char *) space((unsigned) length+1);
if (dangles==1)
{
dangles=2; /* recompute with dangles as in pf_fold() */
min_en = (circ) ? energy_of_circ_struct(string, structure) :
energy_of_struct(string, structure);
dangles=1;
}
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000)
ajWarn("scaling factor %f\n", pf_scale);
(circ) ? init_pf_circ_fold(length) : init_pf_fold(length);
if (cstruc!=NULL)
strncpy(pf_struc, cstruc, length+1);
energy = (circ) ? pf_circ_fold(string, pf_struc) :
pf_fold(string, pf_struc);
if (do_backtrack)
{
ajFmtPrintF(outf,"%s", pf_struc);
ajFmtPrintF(outf," [%6.2f]\n", energy);
}
if ((istty)||(!do_backtrack))
ajFmtPrintF(outf," free energy of ensemble = %6.2f kcal/mol\n",
energy);
if (do_backtrack)
{
plist *pl1,*pl2;
char *cent;
double dist, cent_en;
cent = centroid(length, &dist);
cent_en = (circ) ? energy_of_circ_struct(string, cent) :
energy_of_struct(string, cent);
ajFmtPrintF(outf,"%s {%6.2f d=%.2f}\n", cent, cent_en, dist);
free(cent);
pl1 = make_plist(length, 1e-5);
pl2 = b2plist(structure);
(void) PS_dot_plot_list(string, dotfilea, pl1, pl2, "");
free(pl2);
if (do_backtrack==2)
{
pl2 = stackProb(1e-5);
PS_dot_plot_list(string, dotfileb, pl1, pl2,
"Probabilities for stacked pairs (i,j)(i+1,j-1)");
free(pl2);
}
free(pl1);
free(pf_struc);
}
ajFmtPrintF(outf," frequency of mfe structure in ensemble %g; ",
exp((energy-min_en)/kT));
if (do_backtrack)
ajFmtPrintF(outf,"ensemble diversity %-6.2f", mean_bp_dist(length));
ajFmtPrintF(outf,"\n");
free_pf_arrays();
}
if (cstruc!=NULL)
free(cstruc);
free(string);
free(structure);
ajStrDel(&seqstring);
ajStrDel(&constring);
ajStrDel(&seqname);
ajStrDel(&ensbases);
ajStrDel(&eenergy);
ajStrDel(&edangles);
ajSeqDel(&seq);
ajFileClose(&confile);
ajFileClose(¶mfile);
ajFileClose(&outf);
ajFileClose(&essfile);
/*
ajFileClose(&dotfilea);
ajFileClose(&dotfileb);
*/
if (length<2000) free_arrays();
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[])
{
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) {
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("ggcsi", argc, argv, "GEMBASSY", "1.0.1");
struct soap soap;
struct ns1__gcsiInputParams params;
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr seqid = NULL;
ajint window = 0;
AjBool at = 0;
AjBool purine = 0;
AjBool keto = 0;
AjBool pval = 0;
AjPStr version = NULL;
AjBool accid = ajFalse;
AjPStr tmp = NULL;
AjPStr parse = NULL;
AjPStr gcsi = NULL;
AjPStr sa = NULL;
AjPStr dist = NULL;
AjPStr z = NULL;
AjPStr p = NULL;
AjPStrTok handle = NULL;
char *in0;
char *result;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
window = ajAcdGetInt("window");
at = ajAcdGetBoolean("at");
purine = ajAcdGetBoolean("purine");
keto = ajAcdGetBoolean("keto");
pval = ajAcdGetBoolean("pval");
version = ajAcdGetSelectSingle("gcsi");
accid = ajAcdGetBoolean("accid");
outf = ajAcdGetOutfile("outfile");
params.window = window;
params.at = 0;
params.purine = 0;
params.keto = 0;
params.p = 0;
ajStrToInt(version, &(params.version));
if(at)
params.at = 1;
if(purine)
params.purine = 1;
if(keto)
params.keto = 1;
if(pval)
params.p = 1;
while(ajSeqallNext(seqall, &seq))
{
soap_init(&soap);
inseq = NULL;
ajStrAppendC(&inseq, ">");
ajStrAppendS(&inseq, ajSeqGetNameS(seq));
ajStrAppendC(&inseq, "\n");
ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
in0 = ajCharNewS(inseq);
if (soap_call_ns1__gcsi(
&soap,
NULL,
NULL,
in0,
¶ms,
&result
) == SOAP_OK)
{
tmp = ajStrNew();
parse = ajStrNew();
gcsi = ajStrNew();
sa = ajStrNew();
dist = ajStrNew();
z = ajStrNew();
p = ajStrNew();
ajStrAssignC(&tmp, result);
ajStrExchangeCC(&tmp, "<", "\n");
ajStrExchangeCC(&tmp, ">", "\n");
handle = ajStrTokenNewC(tmp, "\n");
while (ajStrTokenNextParse(&handle, &parse))
{
if (ajStrIsFloat(parse))
{
if(!ajStrGetLen(gcsi))
ajStrAssignS(&gcsi, parse);
else if(!ajStrGetLen(sa))
ajStrAssignS(&sa, parse);
else if(!ajStrGetLen(dist))
ajStrAssignS(&dist, parse);
else if(!ajStrGetLen(z))
ajStrAssignS(&z, parse);
else if(!ajStrGetLen(p))
ajStrAssignS(&p, parse);
}
}
tmp = ajFmtStr("Sequence: %S GCSI: %S SA: %S DIST: %S",
seqid, gcsi, sa, dist);
if(pval)
tmp = ajFmtStr("%S Z: %S P: %S", tmp, z, p);
ajFmtPrintF(outf, "%S\n", tmp);
ajStrDel(&tmp);
ajStrDel(&parse);
ajStrDel(&gcsi);
ajStrDel(&sa);
ajStrDel(&dist);
ajStrDel(&z);
ajStrDel(&p);
}
else
{
soap_print_fault(&soap, stderr);
}
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
AJFREE(in0);
ajStrDel(&inseq);
}
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
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("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;
}
int main(int argc, char **argv)
{
AjPList sigin = NULL; /* Signature input file names. */
AjPStr signame = NULL; /* Name of signature file. */
AjPFile sigf = NULL; /* Signature input file. */
EmbPSignature sig = NULL; /* Signature. */
AjPList siglist = NULL; /* List of signatures. */
AjIList sigiter = NULL; /* Iterator for siglist. */
AjBool sigok = ajFalse; /* True if signature processed ok. */
EmbPHit hit = NULL; /* Hit to store signature-sequence match. */
AjPList hits = NULL; /* List of hits */
AjPList ligands = NULL; /* List of top-scoring ligands. */
AjPSeqall database=NULL; /* Protein sequences to match signature
against. */
AjPSeq seq = NULL; /* Current sequence. */
AjPMatrixf sub =NULL; /* Residue substitution matrix. */
float gapo =0.0; /* Gap insertion penalty. */
float gape =0.0; /* Gap extension penalty. */
AjPStr nterm=NULL; /* Holds N-terminal matching options from
acd. */
ajint ntermi=0; /* N-terminal option as int. */
AjPFile hitsf =NULL; /* Hits output file.
sequence matches. */
AjPDirout hitsdir=NULL; /* Directory of hits files (output). */
AjPFile alignf =NULL; /* Alignment output file. */
AjPDirout aligndir=NULL; /* Directory of alignment files (output). */
AjPFile resultsf =NULL; /* Results file (output). */
AjPDirout resultsdir=NULL; /* Directory of results files (output). */
AjPStr mode = NULL; /* Mode, 1: Patch score mode, 2:
Site score mode. */
ajint modei = 0; /* Selected mode as integer. */
SigPLighit lighit = NULL;
embInitPV("sigscanlig", argc, argv, "SIGNATURE",VERSION);
/* GET VALUES FROM ACD */
sigin = ajAcdGetDirlist("siginfilesdir");
database = ajAcdGetSeqall("dbseqall");
sub = ajAcdGetMatrixf("sub");
gapo = ajAcdGetFloat("gapo");
gape = ajAcdGetFloat("gape");
nterm = ajAcdGetListSingle("nterm");
hitsdir = ajAcdGetOutdir("hitsoutdir");
aligndir = ajAcdGetOutdir("alignoutdir");
resultsdir = ajAcdGetOutdir("resultsoutdir");
mode = ajAcdGetListSingle("mode");
/*Assign N-terminal matching option etc. */
ajFmtScanS(nterm, "%d", &ntermi);
modei = (ajint) ajStrGetCharFirst(mode)-48;
/* READ & PROCESS SIGNATURES */
siglist = ajListNew();
while(ajListPop(sigin, (void **) &signame))
{
/* Read signature files, compile signatures and populate list. */
sigok = ajFalse;
if((sigf = ajFileNewInNameS(signame)))
if((sig = embSignatureReadNew(sigf)))
if(embSignatureCompile(&sig, gapo, gape, sub))
{
sigok=ajTrue;
ajListPushAppend(siglist, sig);
/*
ajFmtPrint("Id: %S\nDomid: %S\nLigid: %S\nns: %d\n"
"sn: %d\nnp: %d\npn: %d\nminpatch: %d\n"
"maxgap: %d\n",
sig->Id, sig->Domid, sig->Ligid, sig->ns,
sig->sn, sig->np, sig->pn, sig->minpatch,
sig->maxgap); */
}
if(!sigok)
{
ajWarn("Could not process %S", signame);
embSignatureDel(&sig);
ajFileClose(&sigf);
ajStrDel(&signame);
continue;
}
ajFileClose(&sigf);
ajStrDel(&signame);
}
ajListFree(&sigin);
/* ALIGN EACH QUERY SEQUENCE TO LIST OF SIGNATURE */
while(ajSeqallNext(database, &seq))
{
/* Do sequence-signature alignment and save results */
hits = ajListNew();
sigiter = ajListIterNew(siglist);
while((sig = (EmbPSignature) ajListIterGet(sigiter)))
{
if(embSignatureAlignSeq(sig, seq, &hit, ntermi))
{
hit->Sig = sig;
ajListPushAppend(hits, hit);
hit=NULL; /* To force reallocation by embSignatureAlignSeq */
}
/* There has to be a hit for each signature for correct
generation of the LHF by sigscanlig_WriteFasta. So push
an empty hit if necessary. 'hit'=NULL forces
reallocation by embSignatureAlignSeq. */
/*
else
{
hit = embHitNew();
ajListPushAppend(hits, hit);
hit=NULL;
}
*/
}
ajListIterDel(&sigiter);
/* Rank-order the list of hits by score */
ajListSort(hits, embMatchinvScore);
/* Write ligand hits & alignment files (output) */
hitsf = ajFileNewOutNameDirS(ajSeqGetNameS(seq), hitsdir);
alignf = ajFileNewOutNameDirS(ajSeqGetNameS(seq), aligndir);
resultsf = ajFileNewOutNameDirS(ajSeqGetNameS(seq), resultsdir);
/* if((!sigscanlig_WriteFasta(hitsf, siglist, hits)))
ajFatal("Bad args to sigscanlig_WriteFasta"); */
if((!sigscanlig_WriteFasta(hitsf, hits)))
ajFatal("Bad args to sigscanlig_WriteFasta");
if((!sigscanlig_SignatureAlignWriteBlock(alignf, hits)))
ajFatal("Bad args to sigscanlig_SignatureAlignWriteBlock");
/* if((!sigscanlig_SignatureAlignWriteBlock(alignf, siglist, hits)))
ajFatal("Bad args to sigscanlig_SignatureAlignWriteBlock"); */
/* Sort list of hits by ligand type and site number.
Process list of ligands and print out. */
ajListSortTwo(hits, embMatchLigid, embMatchSN);
if(modei==1)
ligands = sigscanlig_score_ligands_patch(hits);
else if(modei==2)
ligands = sigscanlig_score_ligands_site(hits);
else
ajFatal("Unrecognised mode");
sigscanlig_WriteResults(ligands, resultsf);
ajFileClose(&hitsf);
ajFileClose(&alignf);
ajFileClose(&resultsf);
/* Memory management */
while(ajListPop(hits, (void **) &hit))
embHitDel(&hit);
ajListFree(&hits);
while(ajListPop(ligands, (void **) &lighit))
sigscanlig_LigHitDel(&lighit);
ajListFree(&ligands);
}
/* MEMORY MANAGEMENT */
while(ajListPop(siglist, (void **) &sig))
embSignatureDel(&sig);
ajListFree(&siglist);
ajSeqallDel(&database);
ajMatrixfDel(&sub);
ajStrDel(&nterm);
ajDiroutDel(&hitsdir);
ajDiroutDel(&aligndir);
ajDiroutDel(&resultsdir);
ajStrDel(&mode);
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", "1.0.1");
struct soap soap;
AjPSeqall seqall;
AjPSeq seq;
AjPStr inseq = NULL;
AjPStr seqid = NULL;
AjPStr tmp = NULL;
AjPStr parse = NULL;
AjPStr numA = NULL;
AjPStr numT = NULL;
AjPStr numG = NULL;
AjPStr numC = NULL;
AjPStrTok handle = NULL;
ajint n;
char *in0;
char *result;
AjBool show = 0;
AjPFile outf = NULL;
seqall = ajAcdGetSeqall("sequence");
outf = ajAcdGetOutfile("outfile");
while(ajSeqallNext(seqall, &seq))
{
soap_init(&soap);
inseq = NULL;
ajStrAppendC(&inseq, ">");
ajStrAppendS(&inseq, ajSeqGetNameS(seq));
ajStrAppendC(&inseq, "\n");
ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
ajStrAssignS(&seqid, ajSeqGetAccS(seq));
in0 = ajCharNewS(inseq);
if(soap_call_ns1__seqinfo(
&soap,
NULL,
NULL,
in0,
&result
) == SOAP_OK)
{
tmp = ajStrNewC(result);
ajStrExchangeCC(&tmp, "<", "\n");
ajStrExchangeCC(&tmp, ">", "\n");
handle = ajStrTokenNewC(tmp, "\n");
while(ajStrTokenNextParse(handle, &parse))
{
if(ajStrIsInt(parse))
if(!numA)
numA = ajStrNewS(parse);
else if(!numT)
numT = ajStrNewS(parse);
else if(!numG)
numG = ajStrNewS(parse);
else if(!numC)
numC = ajStrNewS(parse);
}
if(show)
ajFmtPrint("Sequence: %S A: %S T: %S G: %S C: %S\n",
seqid, numA, numT, numG, numC);
else
ajFmtPrintF(outf, "Sequence: %S A: %S T: %S G: %S C: %S\n",
seqid, numA, numT, numG, numC);
}
else
{
soap_print_fault(&soap, stderr);
}
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
AJFREE(in0);
ajStrDel(&inseq);
}
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&seqid);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* ACD data item variables */
AjPFile oldhmmfile = NULL;
AjPStr format = NULL;
AjPFile newhmmfile = NULL;
/* Housekeeping variables */
AjPStr cmd = NULL;
char option;
/* ACD file processing */
embInitPV("ehmmconvert",argc,argv,"HMMERNEW",VERSION);
oldhmmfile = ajAcdGetInfile("oldhmmfile");
format = ajAcdGetListSingle("format");
newhmmfile = ajAcdGetOutfile("newhmmfile");
/* MAIN APPLICATION CODE */
cmd = ajStrNew();
/* 1. Build hmmconvert 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("hmmconvert"));
/* ACD option only allows one selection */
option = ajStrGetCharFirst(format);
if(option == 'A')
ajStrAppendC(&cmd, " -a ");
else if(option == 'B')
ajStrAppendC(&cmd, " -b ");
else if(option == 'G')
ajStrAppendC(&cmd, " -p ");
else if(option == 'X')
ajStrAppendC(&cmd, " -P ");
/* -A (append) always set but file will be wiped by EMBOSS first unless
append: "Y" is set for "newhmmfile" in the ACD file. */
/* hmmer cannot append to empty file, so only set the -A (append) option
if file was opened for appending to (and therefore was not wiped by
EMBOSS) and is not zero size. */
if(ajFileIsAppend(newhmmfile) && (ajFilenameGetSize(ajFileGetNameS(newhmmfile))!=-1))
ajStrAppendC(&cmd, " -A ");
ajStrAppendC(&cmd, " -F ");
ajFmtPrintAppS(&cmd, " %s %s", ajFileGetNameC(oldhmmfile), ajFileGetNameC(newhmmfile));
/* 2. Close ACD files. */
ajFileClose(&oldhmmfile);
ajFileClose(&newhmmfile);
/* 3. Call hmmconvert */
ajFmtPrint("\n%S\n\n", cmd);
ajSysExecS(cmd);
/* 4. Exit cleanly */
ajStrDel(&cmd);
ajStrDel(&format);
embExit();
return 0;
}
void emboss_getoptions(char *pgm, int argc, char *argv[])
{
AjPStr test = NULL;
AjPStr outputformat = NULL;
AjPStr typeofseq = NULL;
AjPStr justweights = NULL;
AjBool rewrite = false;
long inseed, inseed0;
data = genefreqs;
seq = dna;
bootstrap = false;
jackknife = false;
permute = false;
ild = false;
lockhart = false;
blocksize = 1;
regular = true;
fracsample = 1.0;
all = true;
reps = 100;
weights = false;
mixture = false;
ancvar = false;
categories = false;
justwts = false;
printdata = false;
dotdiff = true;
progress = true;
interleaved = true;
xml = false;
nexus = false;
factors = false;
enzymes = false;
embInitPV(pgm, argc, argv, "PHYLIPNEW",VERSION);
phylofreqs = ajAcdGetFrequencies("infile");
test = ajAcdGetListSingle("test");
if(ajStrMatchC(test, "b")) {
bootstrap = true;
regular = ajAcdGetToggle("regular");
if(regular) fracsample = 1.0;
else {
fracsample = ajAcdGetFloat("fracsample");
fracsample = fracsample/100.0;
}
blocksize = ajAcdGetInt("blocksize");
}
else if(ajStrMatchC(test, "j")) {
jackknife = true;
regular = ajAcdGetToggle("regular");
if(regular) fracsample = 0.5;
else {
fracsample = ajAcdGetFloat("fracsample");
fracsample = fracsample/100.0;
}
}
else if(ajStrMatchC(test, "c")) permute = true;
else if(ajStrMatchC(test, "o")) ild = true;
else if(ajStrMatchC(test, "s")) lockhart = true;
else if(ajStrMatchC(test, "r")) rewrite = true;
if(rewrite) {
if (data == seqs) {
outputformat = ajAcdGetListSingle("rewriteformat");
if(ajStrMatchC(outputformat, "n")) nexus = true;
else if(ajStrMatchC(outputformat, "x")) xml = true;
if( (nexus) || (xml) ) {
typeofseq = ajAcdGetListSingle("seqtype");
if(ajStrMatchC(typeofseq, "d")) seq = dna;
else if(ajStrMatchC(typeofseq, "r")) seq = rna;
else if(ajStrMatchC(typeofseq, "p")) seq = protein;
}
}
}
else{
reps = ajAcdGetInt("reps");
inseed = ajAcdGetInt("seed");
emboss_initseed(inseed, &inseed0, seed);
if(jackknife || bootstrap || permute) {
phyloweights = ajAcdGetProperties("weights");
if(phyloweights) weights = true;
}
if(!permute) {
justweights = ajAcdGetListSingle("justweights");
if(ajStrMatchC(justweights, "j")) justwts = true;
}
}
printdata = ajAcdGetBoolean("printdata");
if(printdata) dotdiff = ajAcdGetBoolean("dotdiff");
progress = ajAcdGetBoolean("progress");
embossoutfile = ajAcdGetOutfile("outfile");
emboss_openfile(embossoutfile, &outfile, &outfilename);
printf("\n bootstrap: %s",(bootstrap ? "true" : "false"));
printf("\njackknife: %s",(jackknife ? "true" : "false"));
printf("\n permute: %s",(permute ? "true" : "false"));
printf("\n lockhart: %s",(lockhart ? "true" : "false"));
printf("\n ild: %s",(ild ? "true" : "false"));
printf("\n justwts: %s \n",(justwts ? "true" : "false"));
} /* emboss_getoptions */
int main(int argc, char *argv[])
{
embInitPV("gentrez", argc, argv, "GEMBASSY", "1.0.1");
struct soap soap;
AjPStr database = NULL;
AjPStr query = NULL;
char *in0;
char *in1;
char *result;
AjPFile outf = NULL;
database = ajAcdGetString("database");
query = ajAcdGetString("query");
outf = ajAcdGetOutfile("outfile");
in0 = ajCharNewS(database);
in1 = ajCharNewS(query);
soap_init(&soap);
if(soap_call_ns1__entrez(
&soap,
NULL,
NULL,
in0,
in1,
&result
) == SOAP_OK)
{
if(result)
{
ajFmtPrintF(outf, "%s", result);
}
else
{
ajFmtPrintF(outf, "No results found.\n");
}
}
else
{
soap_print_fault(&soap, stderr);
}
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf);
AJFREE(in0);
AJFREE(in1);
ajStrDel(&database);
ajStrDel(&query);
embExit();
return 0;
}
