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;
gAssignUniqueName(&filename);
feat = ajSeqGetFeatCopy(seq);
if(!feat)
return ajFalse;
seqout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(seqout,filename))
embExitBad();
ajSeqoutSetFormatS(seqout,ajStrNewC("genbank"));
ajSeqoutWriteSeq(seqout,seq);
ajSeqoutClose(seqout);
ajSeqoutDel(&seqout);
seqfile = ajFileNewInNameS(filename);
ajSysFileUnlinkS(filename);
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(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 ajTrue;
}
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;
}
void ajMessExitDebug(void)
{
ajFileClose(&messDebugFile);
ajStrDel(&messDebugName);
ajFileClose(&messDebugTestFile);
ajStrDel(&messDebugName);
return;
}
AjBool gHttpGetBinS(AjPStr url, AjPFile* outf)
{
AjPFile file = NULL;
AjPStr line = NULL;
AjPStr host = NULL;
AjPStr path = NULL;
AjPStr get = NULL;
ajint port = 80;
ajuint http = 0;
FILE *fp;
AjPRegexp crlf = NULL;
char buf[8];
AjOSysSocket sock;
get = ajStrNew();
ajHttpUrlDeconstruct(url, &port, &host, &path);
while(file==NULL || gHttpRedirect(file, &host, &port, &path))
{
if(ajStrGetCharFirst(path) != '/')
ajStrInsertK(&path, 0, '/');
ajFmtPrintS(&get, "GET http://%S:%d%S HTTP/1.1\r\n", host, port, path);
fp = ajHttpOpen(NULL, host, port, get, &sock);
file = ajFileNewFromCfile(fp);
if(!file)
return ajFalse;
}
ajStrDel(&get);
crlf = ajRegCompC("^\r?\n$");
while(ajReadline(file, &line))
{
if(ajRegExec(crlf, line))
break;
}
while(ajReadbinBinary(file, 1, 1, buf))
{
ajWritebinBinary(*outf, 1, 1, buf);
}
ajFileClose(outf);
ajFileClose(&file);
return ajTrue;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq seq = NULL;
AjPFile primerFile; /* read the primer pairs from a file */
AjPFile outf;
AjPList primerList;
ajint mmp = 0;
embInit("primersearch", argc, argv);
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
primerFile = ajAcdGetInfile("infile");
mmp = ajAcdGetInt("mismatchpercent");
/* build list of forward/reverse primer pairs as read from primerfile */
primerList = ajListNew();
/* read in primers from primerfile, classify and compile them */
primersearch_read_primers(&primerList,primerFile, mmp);
/* check there are primers to be searched */
if(!ajListGetLength(primerList))
{
ajErr("No suitable primers found - exiting");
embExitBad();
return 0;
}
/* query sequences one by one */
while(ajSeqallNext(seqall,&seq))
primersearch_primer_search(primerList, seq);
/* output the results */
primersearch_print_hits(primerList, outf);
/* delete all nodes of list, then the list itself */
ajListMap(primerList, primersearch_free_primer, NULL);
ajListFree(&primerList);
ajListFree(&primerList);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajFileClose(&primerFile);
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)
{
AjPSeqset seqset;
AjPSeqall seqall;
AjPSeq seq;
ajint i = 0;
AjPStr kimout = NULL;
AjPStr dir = NULL;
AjPFile obofile = NULL;
AjPFile resfile = NULL;
AjPDir taxdir = NULL;
embInit("ajtest", argc, argv);
seqall = ajAcdGetSeqall ("sequence");
seqset = ajAcdGetSeqset ("bsequence");
dir = ajAcdGetOutdirName("outdir");
obofile = ajAcdGetInfile ("obofile");
taxdir = ajAcdGetDirectory ("taxdir");
resfile = ajAcdGetInfile ("dbxreffile");
ajUser("Directory '%S'", dir);
ajUser("Set of %d", ajSeqsetGetSize(seqset));
while(ajSeqallNext (seqall, &seq))
{
ajUser ("%3d <%S>", i++, ajSeqGetUsaS(seq));
ajFmtPrintS(&kimout, "kim%d.out", i);
ajtest_kim (kimout, seq);
}
ajSeqDel(&seq);
ajSeqallDel(&seqall);
ajSeqsetDel(&seqset);
ajStrDel(&kimout);
ajStrDel(&dir);
if(taxdir)
ajTaxLoad(taxdir);
ajDirDel(&taxdir);
if(obofile)
ajOboParseObofile(obofile, "");
ajFileClose(&obofile);
if(resfile)
ajResourceParse(resfile, "");
ajFileClose(&resfile);
embExit();
return 0;
}
int main(int argc, Char *argv[])
{ /* main program */
long i;
#ifdef MAC
argc = 1; /* macsetup("Contml",""); */
argv[0] = "Contml";
#endif
init(argc, argv);
emboss_getoptions("fcontml", argc, argv);
progname = argv[0];
ibmpc = IBMCRT;
ansi = ANSICRT;
firstset = true;
doinit();
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n", ith);
if (progress)
printf("\nData set # %ld:\n", ith);
}
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
if (usertree)
for (i = 0; i < MAXSHIMOTREES; i++)
free(l0gf[i]);
}
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("\nDone.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
ajPhyloFreqDel(&phylofreq);
ajPhyloTreeDelarray(&phylotrees);
ajFileClose(&embossoutfile);
ajFileClose(&embossouttree);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* Variable Declarations */
AjPFile inf = NULL;
AjPFile outf = NULL;
AjPStr line = NULL; /* Line from inf */
AjPStr option = NULL;
AjBool doall = AJFALSE;
AjBool doend = AJFALSE;
AjBool doexcess = AJFALSE;
/* ACD File Processing */
embInit("nospace", argc, argv);
inf = ajAcdGetInfile("infile");
outf = ajAcdGetOutfile("outfile");
option = ajAcdGetListSingle("menu");
if(ajStrMatchC(option, "all"))
doall = ajTrue;
else if(ajStrMatchC(option, "end"))
doend = ajTrue;
else if(ajStrMatchC(option, "excess"))
doexcess = ajTrue;
/* Application logic */
line = ajStrNew();
while(ajReadline(inf,&line))
{
if(doall)
ajStrRemoveWhite(&line);
else if(doend)
ajStrTrimWhiteEnd(&line);
else if(doexcess)
ajStrRemoveWhiteExcess(&line);
ajFmtPrintF(outf, "%S\n", line);
}
/* Memory management and exit */
ajFileClose(&inf);
ajFileClose(&outf);
ajStrDel(&line);
ajStrDel(&option);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* Variable declarations */
AjPFile outf = NULL;
AjPXmlall xmlall = NULL;
AjPXml xml = NULL;
/* ACD processing */
embInit("xmltext", argc, argv);
xmlall = ajAcdGetXmlall("xml");
outf = ajAcdGetOutfile("outfile");
while(ajXmlallNext(xmlall, &xml))
{
ajFmtPrintF(outf,"%S",ajXmlGetEntry(xml));
}
/* Memory clean-up and exit */
ajXmlallDel(&xmlall);
ajXmlDel(&xml);
ajFileClose(&outf);
embExit();
return 0;
}
int main(int argc, char **argv)
{
/* Variable declarations */
AjPFile outfile = NULL;
AjPResourceall resourceall = NULL;
AjPResource resource = NULL;
/* ACD processing */
embInit("drtext", argc, argv);
resourceall = ajAcdGetResourceall("resources");
outfile = ajAcdGetOutfile("outfile");
while(ajResourceallNext(resourceall, &resource))
{
ajFmtPrintF(outfile,"%S",ajResourceGetEntry(resource));
}
ajResourceallDel(&resourceall);
ajResourceDel(&resource);
ajFileClose(&outfile);
embExit();
return 0;
}
static void remap_read_equiv(AjPFile *equfile, AjPTable *table,
AjBool commercial)
{
AjPStr line;
AjPStr key;
AjPStr value;
const char *p;
line = ajStrNew();
while(ajReadlineTrim(*equfile,&line))
{
p = ajStrGetPtr(line);
if(!*p || *p=='#' || *p=='!')
continue;
p = ajSysFuncStrtok(p," \t\n");
key = ajStrNewC(p);
p = ajSysFuncStrtok(NULL," \t\n");
value = ajStrNewC(p);
if(!commercial)
ajStrTrimEndC(&value,"*");
ajTablePut(*table,(void *)key, (void *)value);
}
ajFileClose(equfile);
ajStrDel(&line);
return;
}
static void remap_read_file_of_enzyme_names(AjPStr *enzymes)
{
AjPFile file = NULL;
AjPStr line;
const char *p = NULL;
if(ajStrFindC(*enzymes, "@") == 0)
{
ajStrTrimC(enzymes, "@"); /* remove the @ */
file = ajFileNewInNameS(*enzymes);
if(file == NULL)
ajFatal("Cannot open the file of enzyme names: '%S'", enzymes);
/* blank off the enzyme file name and replace with the enzyme names */
ajStrSetClear(enzymes);
line = ajStrNew();
while(ajReadlineTrim(file, &line))
{
p = ajStrGetPtr(line);
if(!*p || *p == '#' || *p == '!')
continue;
ajStrAppendS(enzymes, line);
ajStrAppendC(enzymes, ",");
}
ajStrDel(&line);
ajFileClose(&file);
}
return;
}
static ajuint jaspscan_readmatrix(const AjPStr mfname, float ***matrix)
{
AjPFile inf = NULL;
AjPStr line = NULL;
ajuint i = 0;
ajuint cols = 0;
AJCNEW0(*matrix,4);
line = ajStrNew();
inf = ajFileNewInNameS(mfname);
if(!inf)
ajFatal("Cannot open matrix file %S",mfname);
i = 0;
while(ajReadlineTrim(inf,&line))
{
if(!i)
cols = ajStrParseCountC(line," \n");
(*matrix)[i++] = ajArrFloatLine(line," \n",1,cols);
}
ajStrDel(&line);
ajFileClose(&inf);
return cols;;
}
void embIepPkRead(double *pK)
{
AjPFile inf = NULL;
AjPStr line;
const char *p;
double amino = 8.6;
double carboxyl = 3.6;
char ch;
ajint i;
inf = ajDatafileNewInNameC(PKFILE);
if(!inf)
ajFatal("%s file not found",PKFILE);
for(i=0;i<EMBIEPSIZE;++i)
pK[i]=0.0;
line = ajStrNew();
while(ajReadline(inf,&line))
{
p = ajStrGetPtr(line);
if(*p=='#' || *p=='!' || *p=='\n' || *p=='\r')
continue;
if(ajStrPrefixCaseC(line,"Amino"))
{
p = ajSysFuncStrtok(p," \t\n\r");
p = ajSysFuncStrtok(NULL," \t\n\r");
sscanf(p,"%lf",&amino);
continue;
}
if(ajStrPrefixCaseC(line,"Carboxyl"))
{
p = ajSysFuncStrtok(p," \t\n\r");
p = ajSysFuncStrtok(NULL," \t\n\r");
sscanf(p,"%lf",&carboxyl);
continue;
}
p = ajSysFuncStrtok(p," \t\n\r");
ch = ajSysCastItoc(toupper((ajint)*p));
p = ajSysFuncStrtok(NULL," \t\n\r");
sscanf(p,"%lf",&pK[ajBasecodeToInt(ch)]);
}
pK[EMBIEPAMINO] = amino;
pK[EMBIEPCARBOXYL] = carboxyl;
ajStrDel(&line);
ajFileClose(&inf);
return;
}
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;
}
static void jaspextract_writematrixfile(const AjPTable mtable,
const AjPStr directory)
{
AjPStr wild = NULL;
AjPList flist = NULL;
AjPStr key = NULL;
AjPStr fname = NULL;
AjPStr dest = NULL;
const AjPStr value = NULL;
AjPFile outf = NULL;
const char *p = NULL;
char *q = NULL;
wild = ajStrNewC("*.pfm");
flist = ajListNew();
key = ajStrNew();
dest = ajStrNew();
ajFmtPrintS(&dest,"%S%c%s",directory,SLASH_CHAR,MATRIXFILE);
outf = ajFileNewOutNameS(dest);
if(!outf)
ajFatal("Cannot open output file %S",dest);
ajFilelistAddPathWild(flist, directory, wild);
while(ajListPop(flist,(void**)&fname))
{
ajFilenameTrimPath(&fname);
p = ajStrGetPtr(fname);
q = strrchr(p,(int)'.');
ajStrAssignSubC(&key,p,0,q-p-1);
value = ajTableFetchS(mtable, key);
if(value)
ajFmtPrintF(outf,"%S",value);
ajStrDel(&fname);
}
ajFileClose(&outf);
ajStrDel(&wild);
ajStrDel(&dest);
ajStrDel(&key);
ajListFree(&flist);
return;
}
static void jaspextract_readmatrixlist(AjPTable mtable, const AjPStr directory)
{
const AjPStr datadir = NULL;
AjPStr matrixfile = NULL;
AjPFile inf = NULL;
AjPStr line = NULL;
AjPStr key = NULL;
AjPStr value = NULL;
matrixfile = ajStrNew();
datadir = ajDatafileValuePath();
if(!datadir)
ajFatal("jaspextract: Cannot determine the EMBOSS data directory");
ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE);
if(!ajFilenameExistsRead(matrixfile))
ajFatal("jaspextract: Directory (%S) doesn't appear to be a JASPAR "
"one\nNo matrix_list.txt file found",directory);
inf = ajFileNewInNameS(matrixfile);
if(!inf)
ajFatal("Cannot open input file: %S",matrixfile);
while(ajReadline(inf,&line))
{
key = ajStrNew();
if(ajFmtScanS(line,"%S",&key) != 1)
{
ajStrDel(&key);
continue;
}
value = ajStrNew();
ajStrAssignS(&value,line);
ajTablePut(mtable,(void *)key, (void *)value);
}
ajFileClose(&inf);
ajStrDel(&matrixfile);
ajStrDel(&line);
return;
}
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)
{
/* Variable Declarations */
AjPFile outf;
AjPStr code = NULL;
char code1;
ajuint i;
ajuint iend;
/* ACD File Processing */
embInit("infobase", argc, argv);
code = ajAcdGetString("code");
outf = ajAcdGetOutfile("outfile");
/* Application logic */
ajStrFmtUpper(&code);
iend = ajStrGetLen(code);
ajFmtPrintF(outf, "%4s %-10s %-10s %s\n",
"Code", "Ambiguity", "Complement", "Mnemonic");
for(i=0;i<iend;i++)
{
code1=ajStrGetCharPos(code,i);
if(ajBaseExistsChar(code1))
{
ajFmtPrintF(outf, "%-4c %-10S %-10c %S\n",
code1, ajBaseGetCodes(code1),
ajBaseAlphacharComp(code1),
ajBaseGetMnemonic(code1));
}
else
{
ajFmtPrintF(outf, "%-4c %-10s %-10c %s\n",
code1, ".",
'.',
"invalid");
}
}
/* Memory management and exit */
ajStrDel(&code);
ajFileClose(&outf);
embExit();
return 0;
}
static void assemoutBamIndex(AjPOutfile outf)
{
char *fname = ajCharNewC(ajFileGetNameC(ajOutfileGetFile(outf)));
AjPSeqBamBgzf gzfile = outf->OutData;
ajSeqBamBgzfClose(gzfile);
ajFileClose(&outf->File);
ajBamIndexBuild(fname);
AJFREE(fname);
return;
}
static void dastestSaveMappedFeatures(const AjPFeattable fttable,
const AjPStr ffname,
AjPFile outf, ajint maxfeatures)
{
AjPFeature feature = NULL;
AjIList iterfts = NULL;
AjPFeattabOut ftout = NULL;
AjPFile ffile = NULL;
AjPStr ffnamee = ajStrNew();
ajint i=0;
if (fttable == NULL)
{
ajWarn("null feature table, %S", ffname);
return;
}
ajFmtPrintS(&ffnamee, "%S.mapped.dasgff", ffname);
ffile = ajFileNewOutNameS(ffnamee);
iterfts = ajListIterNew(fttable->Features);
ftout= ajFeattabOutNewCSF("gff3",NULL,"",ffile);
ajFmtPrintF(outf, "Number of features %d\n",
ajListGetLength(fttable->Features));
while(!ajListIterDone(iterfts) && i++ < maxfeatures)
{
feature = ajListIterGet(iterfts);
ajFmtPrintF(outf,
"feature id:%S orientation:%c start:%d stop:%d\n",
feature->Label,
feature->Strand,
feature->Start, feature->End);
}
ajListIterDel(&iterfts);
ajFeattableWriteDasgff(ftout, fttable);
ajFeattabOutDel(&ftout);
ajFileClose(&ffile);
ajStrDel(&ffnamee);
return;
}
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)
{
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPCod codon;
AjPStr substr;
ajint beg;
ajint end;
ajint ccnt;
embInit("cusp", argc, argv);
seqall = ajAcdGetSeqall("sequence");
outf = ajAcdGetOutfile("outfile");
ccnt = 0;
substr = ajStrNew();
codon = ajCodNewCodenum(0);
ajCodSetNameS(codon, ajFileGetPrintnameS(outf));
while(ajSeqallNext(seqall, &seq))
{
beg = ajSeqallGetseqBegin(seqall);
end = ajSeqallGetseqEnd(seqall);
ajStrAssignSubS(&substr,ajSeqGetSeqS(seq),beg-1,end-1);
ajCodSetTripletsS(codon,substr,&ccnt);
}
ajCodCalcUsage(codon,ccnt);
ajCodSetDescC(codon, "CUSP codon usage file");
ajCodWrite(codon, outf);
ajFileClose(&outf);
ajStrDel(&substr);
ajCodDel(&codon);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
embExit();
return 0;
}
static void dbiblast_memfclosefile(PMemFile* pfd)
{
PMemFile fd;
if(!pfd)
return;
if(!*pfd)
return;
fd = *pfd;
ajFileClose(&fd->File);
ajStrDel(&fd->Name);
AJFREE(*pfd);
return;
}
static void ajtest_kim (const AjPStr seqout_name, const AjPSeq subseq)
{
AjPFile seqout_file = ajFileNewOutNameS(seqout_name);
AjPSeqout named_seqout = ajSeqoutNewFile(seqout_file);
AjPStr format_str = ajStrNew();
ajStrAssignC(&format_str, "embl");
ajSeqoutSetFormatS(named_seqout, format_str);
ajSeqoutWriteSeq(named_seqout, subseq);
ajSeqoutDel(&named_seqout);
ajFileClose(&seqout_file);
ajStrDel(&format_str);
return;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq seq;
AjPTable table = 0;
AjPFile outf;
ajint wordsize;
ajint mincount;
embInit("wordcount", argc, argv);
seqall = ajAcdGetSeqall("sequence1");
wordsize = ajAcdGetInt("wordsize");
outf = ajAcdGetOutfile("outfile");
mincount = ajAcdGetInt("mincount");
embWordLength(wordsize);
while (ajSeqallNext(seqall, &seq))
{
embWordGetTable(&table, seq); /* get table of words */
}
embWordPrintTableFI(table, mincount, outf); /* print table of words */
/*
** test if table can be added to
** if(getWordTable(&table, seq, wordcount)) ?? get table of words ??
** {
** printWordTable(table); ?? print table of words ??
** }
*/
embWordFreeTable(&table); /* free table of words */
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajFileClose(&outf);
embExit();
return 0;
}
static void emira_doinfiles(AjPStr *cl, AjPTable table)
{
ajuint i;
AjPStr squal = NULL;
AjPStr prefix = NULL;
AjPStr key = NULL;
AjPStr value = NULL;
AjPFile infile = NULL;
prefix = ajStrNew();
key = ajStrNew();
i = 0;
while(mirainfiles[i].qname)
{
infile = ajAcdGetInfile(mirainfiles[i].qname);
if(infile)
squal = ajStrNewS(ajFileGetName(infile));
else
squal = ajStrNewS(ajAcdGetValueDefault(mirainfiles[i].qname));
ajStrAssignC(&key,mirainfiles[i].mname);
ajStrAssignC(&prefix,"");
value = ajTableFetch(table, key);
if(value)
ajStrAssignS(&prefix,value);
if(!ajStrMatchC(squal,mirainfiles[i].def))
ajFmtPrintAppS(cl," -%S%s=%S",prefix,mirainfiles[i].mname,
squal);
ajStrDel(&squal);
ajFileClose(&infile);
++i;
}
ajStrDel(&key);
ajStrDel(&prefix);
return;
}
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;
}
static void notseq_readfile(const AjPStr exclude, AjPStr *pattern)
{
AjPFile file = NULL;
AjPStr line;
AjPStr filename = NULL;
const char *p = NULL;
if(ajStrFindC(exclude, "@") != 0)
{
ajStrAssignS(pattern, exclude);
}
else
{
ajStrAssignS(&filename, exclude);
ajStrTrimC(&filename, "@"); /* remove the @ */
file = ajFileNewInNameS(filename);
if(file == NULL)
ajFatal("Cannot open the file of sequence names: '%S'", filename);
/* blank off the file name and replace with the sequence names */
ajStrSetClear(pattern);
line = ajStrNew();
while(ajReadlineTrim(file, &line))
{
p = ajStrGetPtr(line);
if(!*p || *p == '#' || *p == '!')
continue;
ajStrAppendS(pattern, line);
ajStrAppendC(pattern, ",");
}
ajStrDel(&line);
ajStrDel(&filename);
ajFileClose(&file);
}
return;
}
