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; }