static void acdrelations_readtypefile
(AjPFile inf,
PKtype *T)
{
AjPStr line = NULL;
PKtypedat dattmp = NULL;
AjPList datlist = NULL;
if(!T)
ajFatal("Null arg error 1 in acdrelations_readtypefile");
if(!inf)
ajFatal("Null arg error 3 in acdrelations_readtypefile");
/* Allocate memory */
line = ajStrNew();
datlist = ajListNew();
/* Read data from file */
while(ajReadline(inf,&line))
{
/* Discard comment lines */
if(ajStrPrefixC(line,"#"))
continue;
/* Create object for holding line */
dattmp = ajKtypedatNew();
/* Tokenise line delimited by '|'
Parse first token (value of knowntype: attribute) */
ajStrAssignS(&dattmp->ktype, ajStrParseC(line, "|"));
ajStrRemoveSetC(&dattmp->ktype, "_");
ajStrRemoveWhite(&dattmp->ktype);
/* Parse second token (ACD datatype) */
ajStrAssignS(&dattmp->acdtype, ajStrParseC(NULL, "|"));
/* Parse third token (EDAM relations: value ) */
ajStrAssignS(&dattmp->edam, ajStrParseC(NULL, "|"));
/* Push line onto list */
ajListPushAppend(datlist, dattmp);
}
/* Write PKtype structure */
((*T)->n) = ajListToarray(datlist, (void***) &((*T)->dat));
/* Free memory */
ajStrDel(&line);
ajListFree(&datlist);
return;
}
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("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[])
{
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;
}
/* @funcstatic acdrelations_procacdfile ***************************************
**
** Process ACD file and write new ACD file with new relations: attributes
** added (replaced if necessary).
**
** @param [r] inf [AjPFile] ACD input file
** @param [r] outf [AjPFile] ACD output file
** @param [r] P [PEdam] edam object
** @param [r] T [PKtype] ktype object
** @return [void]
** @@
******************************************************************************/
static void acdrelations_procacdfile
(AjPFile inf,
AjPFile outf,
PEdam P,
PKtype T)
{
AjPStr line = NULL;
AjPStr tok = NULL;
AjPStr acdtype = NULL;
AjPStr strtmp = NULL;
AjPList strlist = NULL;
AjPStr *strarr = NULL;
ajint nstr = 0;
/* Allocate memory */
line = ajStrNew();
tok = ajStrNew();
acdtype = ajStrNew();
strlist = ajListstrNew();
/* Read next line */
while(ajReadline(inf,&line))
{
ajFmtScanS(line, "%S", &tok);
/* Write application definition or section definition out as-is */
if(ajStrMatchC(tok, "application:") ||
ajStrMatchC(tok, "section:"))
{
ajFmtPrintF(outf, "%S", line);
while(ajReadline(inf,&line))
{
ajFmtPrintF(outf, "%S", line);
ajFmtScanS(line, "%S", &tok);
if(ajStrMatchC(tok, "]"))
break;
}
}
/* Write variables, endsection definitions and comments out as-is */
else if(ajStrMatchC(tok, "variable:") ||
ajStrMatchC(tok, "endsection:") ||
ajStrMatchC(tok, "#"))
ajFmtPrintF(outf, "%S", line);
/* Write out blank lines as-is */
else if (!ajFmtScanS(line, "%S", &tok))
ajFmtPrintF(outf, "%S", line);
/* Process data definition */
else
/* First line of data definition */
{
/* Process and write datatype line */
ajFmtPrintF(outf, "%S", line);
ajFmtScanS(line, "%S", &acdtype);
ajStrRemoveSetC(&acdtype, ":");
/* Process subsequent (attribute) lines */
while(ajReadline(inf,&line))
{
strtmp = ajStrNew();
ajStrAssignS(&strtmp, line);
ajStrRemoveWhite(&strtmp);
ajListstrPushAppend(strlist, strtmp);
ajFmtScanS(line, "%S", &tok);
/* Reached end of data definition */
if(ajStrMatchC(tok, "]"))
{
nstr = ajListstrToarray(strlist, &strarr);
/* Write relations: line */
acdrelations_writerelations(outf, acdtype, strarr, nstr, P, T);
AJFREE(strarr);
ajListstrFreeData(&strlist);
strlist = ajListstrNew();
ajFmtPrintF(outf, "%S", line);
break;
}
/* Ignore existing relations: lines */
else if(ajStrMatchC(tok, "relations:"))
continue;
ajFmtPrintF(outf, "%S", line);
}
}
}
/* Free memory */
ajStrDel(&line);
ajStrDel(&tok);
ajStrDel(&acdtype);
ajListstrFreeData(&strlist);
return;
}
