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("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("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[]) { 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[]) { 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("greporiter", argc, argv, "GEMBASSY", "1.0.3"); AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; AjBool accid = ajFalse; AjPStr restid = NULL; AjPStr seqid = NULL; AjPStr base = NULL; AjPStr url = NULL; AjBool oriloc = 0; AjBool gcskew = 0; AjBool dbonly = 0; ajint difthreshold = 0; AjPFile outf = NULL; AjPFile tmpfile = NULL; AjPStr tmpname = NULL; AjPStr fstname = NULL; AjPFilebuff tmp = NULL; AjPStr line = NULL; AjPSeqout tmpout = NULL; AjPRegexp regex; AjPStr ori = NULL; AjPStr ter = NULL; seqall = ajAcdGetSeqall("sequence"); difthreshold = ajAcdGetInt("difthreshold"); oriloc = ajAcdGetBoolean("oriloc"); gcskew = ajAcdGetBoolean("gcskew"); dbonly = ajAcdGetBoolean("dbonly"); accid = ajAcdGetBoolean("accid"); outf = ajAcdGetOutfile("outfile"); base = ajStrNewC("rest.g-language.org"); gAssignUniqueName(&tmpname); gAssignUniqueName(&fstname); ajStrAppendC(&fstname, ".fasta"); while(ajSeqallNext(seqall, &seq)) { inseq = ajStrNew(); tmpout = ajSeqoutNew(); if(!accid) { if(gFormatGenbank(seq, &inseq)) { tmpfile = ajFileNewOutNameS(tmpname); if(!tmpfile) { ajDie("Output file (%S) open error\n", tmpname); } ajFmtPrintF(tmpfile, "%S", inseq); ajFileClose(&tmpfile); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); } else { if(!ajSeqoutOpenFilename(tmpout, fstname)) { embExitBad(); } ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta")); ajSeqoutWriteSeq(tmpout, seq); ajSeqoutClose(tmpout); ajSeqoutDel(&tmpout); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, fstname, &restid); ajStrDel(&url); ajSysFileUnlinkS(fstname); } } ajStrAssignS(&seqid, ajSeqGetAccS(seq)); if(ajStrGetLen(seqid) == 0) { ajStrAssignS(&seqid, ajSeqGetNameS(seq)); } if(ajStrGetLen(seqid) == 0) { ajWarn("No valid header information\n"); } if(accid) { ajStrAssignS(&restid, seqid); if(ajStrGetLen(seqid) == 0) { ajDie("Cannot proceed without header with -accid\n"); } if(!gValID(seqid)) { ajDie("Invalid accession ID:%S, exiting\n", seqid); } } url = ajStrNew(); ajFmtPrintS(&url, "http://%S/%S/rep_ori_ter/oriloc=%d/gcskew=%d/" "difthreshold=%d/dbonly=%d/", base, restid, oriloc, gcskew, difthreshold, dbonly); if(!gFilebuffURLS(url, &tmp)) { ajDie("Failed to download result from:\n%S\n", url); } ajBuffreadLine(tmp, &line); regex = ajRegCompC("([0-9]+),([0-9]+)"); if(ajRegExec(regex, line)) { if(ajRegSubI(regex, 1, &ori), ajRegSubI(regex, 2, &ter)) { ajFmtPrint("%S Origin: %S Terminus %S\n", seqid, ori, ter); } } ajStrDel(&url); ajStrDel(&restid); ajStrDel(&seqid); ajStrDel(&inseq); } ajFileClose(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&base); embExit(); return 0; }
int main(int argc, char *argv[]) { embInitPV("genret", argc, argv, "GEMBASSY", "1.0.3"); AjPSeqall seqall; AjPSeq seq = NULL; AjPStr inseq = NULL; AjPStr gene = NULL; AjPStr access = NULL; AjBool accid = ajTrue; AjPStr argument = NULL; AjPFile outfile = NULL; AjPStr seqid = NULL; AjPStr restid = NULL; AjBool valid = ajFalse; AjBool isseq = ajFalse; AjBool isgbk = ajFalse; AjPFilebuff buff = NULL; AjPFile tmpfile = NULL; AjPStr tmpname = NULL; AjPStr regexstr = NULL; AjPStrTok token = NULL; AjPRegexp regex = NULL; AjPStr url = NULL; AjPStr base = NULL; AjPStr head = NULL; AjPStr line = NULL; seqall = ajAcdGetSeqall("sequence"); access = ajAcdGetString("access"); gene = ajAcdGetString("gene"); argument = ajAcdGetString("argument"); accid = ajAcdGetBoolean("accid"); outfile = ajAcdGetOutfile("outfile"); if( ajStrMatchC(access, "translation") || ajStrMatchC(access, "get_exon") || ajStrMatchC(access, "get_exons") || ajStrMatchC(access, "get_cdsseq") || ajStrMatchC(access, "get_gbkseq") || ajStrMatchC(access, "get_geneseq") || ajStrMatchC(access, "get_intron") || ajStrMatchC(access, "getseq") || ajStrMatchC(access, "seq") || ajStrMatchC(access, "around_startcodon") || ajStrMatchC(access, "around_stopcodon") || ajStrMatchC(access, "before_startcodon") || ajStrMatchC(access, "before_stopcodon") || ajStrMatchC(access, "after_startcodon") || ajStrMatchC(access, "after_stopcodon") ) { isseq = ajTrue; } else if(ajStrMatchC(access, "annotate") || ajStrMatchC(access, "output")) { isgbk = ajTrue; } else { ajFmtPrintF(outfile, "gene,%S\n", access); } base = ajStrNewC("rest.g-language.org"); ajStrExchangeCC(&argument, " ", "/"); ajStrExchangeCC(&argument, ",", "/"); ajStrExchangeCC(&argument, "\t", "/"); ajStrExchangeCC(&argument, "\r", "/"); ajStrExchangeCC(&argument, "\n", "/"); if(ajStrMatchC(gene, "*")) { ajStrInsertK(&gene, 0, '.'); } if(ajStrPrefixC(gene, "@") || ajStrPrefixC(gene, "list::")) { ajStrExchangeCC(&gene, "@", ""); ajStrExchangeCC(&gene, "list::", ""); ajStrAssignS(&tmpname, gene); tmpfile = ajFileNewInNameS(tmpname); if(!tmpfile) { ajDie("List file (%S) open error\n", tmpname); } gene = ajStrNew(); while(ajReadline(tmpfile, &line)) { ajStrAppendS(&gene, line); } ajFileClose(&tmpfile); ajStrDel(&tmpname); ajStrDel(&line); } tmpname = ajStrNew(); gAssignUniqueName(&tmpname); while(ajSeqallNext(seqall, &seq)) { inseq = ajStrNew(); if(!accid) { if(gFormatGenbank(seq, &inseq)) { tmpfile = ajFileNewOutNameS(tmpname); if(!tmpfile) { ajDie("Output file (%S) open error\n", tmpname); } ajFmtPrintF(tmpfile, "%S", inseq); ajFileClose(&tmpfile); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); } else { ajWarn("Sequence does not have features\n" "Proceeding with sequence accession ID\n"); accid = ajTrue; } } ajStrAssignS(&seqid, ajSeqGetAccS(seq)); if(ajStrGetLen(seqid) == 0) { ajStrAssignS(&seqid, ajSeqGetNameS(seq)); } if(ajStrGetLen(seqid) == 0) { ajWarn("No valid header information\n"); } if(accid) { ajStrAssignS(&restid, seqid); if(ajStrGetLen(seqid) == 0) { ajDie("Cannot proceed without header with -accid\n"); } if(!gValID(seqid)) { ajDie("Invalid accession ID:%S, exiting\n", seqid); } } url = ajStrNew(); if(isgbk) { ajFmtPrintS(&url, "http://%S/%S/%S", base, restid, access); } else { ajFmtPrintS(&url, "http://%S/%S/*/%S/%S", base, restid, access, argument); } if(!gFilebuffURLS(url, &buff)) { ajDie("GET error from %S\n", url); } while(ajBuffreadLine(buff, &line)) { if(isgbk){ ajFmtPrintF(outfile, "%S", line); continue; } ajStrRemoveLastNewline(&line); regex = ajRegCompC("^>"); if(ajRegExec(regex, line)) { head = ajStrNew(); ajStrAssignS(&head, line); ajStrTrimStartC(&head, ">"); valid = ajFalse; token = ajStrTokenNewC(ajStrNewS(gene), " ,\t\r\n"); while(ajStrTokenNextParse(token, ®exstr)) { if(ajStrGetLen(regexstr)) { regex = ajRegComp(regexstr); if(ajRegExec(regex, line)) { valid = ajTrue; if(ajStrIsAlnum(regexstr)) { ajStrExchangeSC(&gene, regexstr, ""); } } ajRegFree(®ex); } } } else { if(valid) { if(isseq) { ajStrFmtWrap(&line, 60); ajFmtPrintF(outfile, ">%S\n%S\n", head, line); } else { ajFmtPrintF(outfile, "%S,%S\n", head, line); } valid = ajFalse; } } } ajFileClose(&outfile); ajStrDel(&restid); ajStrDel(&seqid); ajStrDel(&inseq); } ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&access); ajStrDel(&gene); embExit(); }
int main(int argc, char *argv[]) { embInitPV("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; }
static AjBool assemoutWriteSamAlignment(AjPFile outf, const AjPAssemRead r, AjPAssemContig const * contigs, ajint ncontigs) { AjPAssemTag t = NULL; AjIList l = NULL; AjPStr qualstr = NULL; AjPStr tmp = NULL; ajint POS = 0; AjPStr CIGAR = NULL; const char* RNEXT = NULL; AjPStr SEQ = NULL; AjPStr QUAL = NULL; AjPStr SEQunpadded = NULL; AjPStr QUALunpadded = NULL; AjPStr consensus = NULL; AjBool rc= ajFalse; AjBool ret = ajTrue; const char* refseq = NULL; const AjPAssemContig contig = NULL; ajuint k = 0; if(r->Reference>=ncontigs) ajDie("assemoutWriteSamAlignment: reference sequence number" " '%d' is larger than or equal to known number of reference" " sequences '%d'. Problem while processing read '%S'.", r->Reference, ncontigs, r->Name); contig = (r->Reference==-1 ? NULL : contigs[r->Reference]); ajStrAssignRef(&SEQ, r->Seq); consensus = contig==NULL? NULL : contig->Consensus; if (r->Rnext==-1) RNEXT= "*"; else if(r->Rnext==r->Reference) RNEXT = "="; else RNEXT = ajStrGetPtr(contigs[r->Rnext]->Name); if (r->Flag & BAM_FREVERSE) { rc = ajTrue; qualstr = ajStrNewS(r->SeqQ); if(!r->Reversed) { ajStrReverse(&qualstr); ajSeqstrReverse(&SEQ); } QUAL = qualstr; POS = r->y1; ajStrAssignSubS(&tmp, SEQ, ajStrGetLen(r->Seq) - r->y2, ajStrGetLen(r->Seq) - r->x2 ); } else { rc= ajFalse; POS = r->x1; QUAL = r->SeqQ; ajStrAssignSubS(&tmp, SEQ, r->x2-1, r->y2-1 ); } if(r->Cigar==NULL && consensus) { refseq = ajStrGetPtr(consensus) + (rc ? r->y1-1 : r->x1-1); CIGAR = assemoutMakeCigar(refseq, ajStrGetPtr(tmp)); SEQunpadded = ajStrNewRes(ajStrGetLen(SEQ)); QUALunpadded = ajStrNewRes(ajStrGetLen(SEQ)); for(k=0; k< ajStrGetLen(SEQ); k++) { if (ajStrGetCharPos(SEQ, k) == '*') continue; ajStrAppendK(&SEQunpadded, ajStrGetCharPos(SEQ, k)); ajStrAppendK(&QUALunpadded, ajStrGetCharPos(QUAL, k)); } ajDebug("cigar: %S\n", CIGAR); ajStrAssignS(&tmp, CIGAR); if(rc) { if(r->y2 < (ajint)ajStrGetLen(SEQ)) ajFmtPrintS(&CIGAR, "%dS%S", ajStrGetLen(SEQ) - r->y2, tmp); if(r->x2 > 1) ajFmtPrintAppS(&CIGAR, "%dS", r->x2 - 1); } else { if(r->x2 > 1) ajFmtPrintS(&CIGAR, "%dS%S", r->x2 - 1, tmp); if(r->y2 < (ajint)ajStrGetLen(SEQ)) ajFmtPrintAppS(&CIGAR, "%dS", ajStrGetLen(SEQ) - r->y2); } ajStrDel(&tmp); } else if(r->Cigar==NULL) { ajErr("both CIGAR string and consensus sequence not available"); ret = ajFalse; ajStrAssignK(&CIGAR, '*'); } else if(!ajStrGetLen(r->Cigar)) ajStrAssignK(&CIGAR, '*'); else if(ajStrGetLen(r->Cigar)) { if(!ajStrGetLen(SEQ)) ajStrAssignK(&SEQ, '*'); if(!ajStrGetLen(QUAL)) ajStrAssignK(&QUAL, '*'); } ajStrDel(&tmp); ajFmtPrintF(outf, "%S\t%d\t%s\t%d\t%d\t%S\t%s\t%Ld\t%d\t%S\t%S", r->Name, r->Flag, (contig==NULL ? "*" : ajStrGetPtr(contig->Name)), POS, r->MapQ, (CIGAR ? CIGAR : r->Cigar), RNEXT, r->Pnext, r->Tlen, (r->Cigar ? SEQ : SEQunpadded), (r->Cigar ? QUAL : QUALunpadded)); l = ajListIterNewread(r->Tags); while (!ajListIterDone(l)) { t = ajListIterGet(l); /* TODO: array type, 'B' */ /* In SAM, all single integer types are mapped to int32_t [SAM spec] */ ajFmtPrintF(outf, "\t%S:%c:", t->Name, (t->type == 'c' || t->type == 'C' || t->type == 's' || t->type == 'S' || t->type == 'I') ? 'i' : t->type ); if(t->x1 || t->y1) ajFmtPrintF(outf, " %u %u", t->x1, t->y1); if(t->Comment && ajStrGetLen(t->Comment)>0) ajFmtPrintF(outf, "%S", t->Comment); } ajListIterDel(&l); ajFmtPrintF(outf, "\n"); if(qualstr) ajStrDel(&qualstr); ajStrDel(&SEQ); ajStrDel(&CIGAR); ajStrDel(&SEQunpadded); ajStrDel(&QUALunpadded); return ret; }
int main(int argc, char *argv[]) { embInitPV("gldabias", argc, argv, "GEMBASSY", "1.0.1"); AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; ajint coefficients = 0; AjPStr variable = NULL; AjBool accid = ajFalse; AjPStr restid = NULL; AjPStr seqid = NULL; AjPStr base = NULL; AjPStr url = NULL; AjPFile tmpfile = NULL; AjPStr tmpname = NULL; AjPFilebuff tmp = NULL; AjPStr line = NULL; AjPFile outf = NULL; seqall = ajAcdGetSeqall("sequence"); coefficients = ajAcdGetInt("coefficients"); variable = ajAcdGetSelectSingle("variable"); accid = ajAcdGetBoolean("accid"); outf = ajAcdGetOutfile("outfile"); base = ajStrNewC("rest.g-language.org"); gAssignUniqueName(&tmpname); while(ajSeqallNext(seqall, &seq)) { inseq = NULL; if(!accid) { if(gFormatGenbank(seq, &inseq)) { tmpfile = ajFileNewOutNameS(tmpname); if(!tmpfile) { ajDie("Output file (%S) open error\n", tmpname); } ajFmtPrintF(tmpfile, "%S", inseq); ajFileClose(&tmpfile); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); } else { ajDie("Sequence does not have features\n" "Proceeding with sequence accession ID\n"); accid = ajTrue; } } if(accid) { ajStrAssignS(&restid, ajSeqGetAccS(seq)); if(!ajStrGetLen(restid)) { ajStrAssignS(&restid, ajSeqGetNameS(seq)); } if(!ajStrGetLen(restid)) { ajDie("No valid header information\n"); } } ajStrAssignS(&seqid, ajSeqGetAccS(seq)); url = ajStrNew(); ajFmtPrintS(&url, "http://%S/%S/lda_bias/coefficients=%d/variable=%S", base, restid, coefficients, variable); if(!gFilebuffURLS(url, &tmp)) { ajDie("Failed to download result from:\n%S\n", url); } ajBuffreadLine(tmp, &line); ajStrRemoveSetC(&line, "\n"); ajFmtPrintF(outf, "Sequence: %S LDA-BIAS: %S\n", seqid, line); ajStrDel(&url); ajStrDel(&inseq); } ajFileClose(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&seqid); embExit(); return 0; }
int main(int argc, char *argv[]) { embInitPV("gcgr", argc, argv, "GEMBASSY", "1.0.1"); struct soap soap; struct ns1__cgrInputParams params; AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; AjPStr seqid = NULL; ajint width = 0; AjPFile outf = NULL; AjPStr filename = NULL; AjPStr outfname = NULL; AjPStr format = NULL; ajint i; char *in0; char *result; seqall = ajAcdGetSeqall("sequence"); width = ajAcdGetInt("width"); filename = ajAcdGetString("goutfile"); format = ajAcdGetString("format"); params.width = width; i = 0; while(ajSeqallNext(seqall, &seq)) { soap_init(&soap); inseq = NULL; ajStrAppendC(&inseq, ">"); ajStrAppendS(&inseq, ajSeqGetAccS(seq)); ajStrAppendC(&inseq, "\n"); ajStrAppendS(&inseq, ajSeqGetSeqS(seq)); ajStrAssignS(&seqid, ajSeqGetAccS(seq)); in0 = ajCharNewS(inseq); if(soap_call_ns1__cgr( &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, "png")) { if(!gHttpConvertC(result, &outf, ajStrNewC("png"), 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(&filename); embExit(); }
int main(int argc, char *argv[]) { embInitPV("gseqinfo", argc, argv, "GEMBASSY", "1.0.3"); AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; AjPStr ori = NULL; AjPStr ter = NULL; AjPStr restid = NULL; AjPStr seqid = NULL; AjPStr base = NULL; AjPStr url = NULL; AjPStr tmpname = NULL; AjPSeqout tmpout = NULL; AjPFile outf = NULL; seqall = ajAcdGetSeqall("sequence"); outf = ajAcdGetOutfile("outfile"); base = ajStrNewC("rest.g-language.org"); gAssignUniqueName(&tmpname); ajStrAppendC(&tmpname, ".fasta"); while(ajSeqallNext(seqall, &seq)) { tmpout = ajSeqoutNew(); if(!ajSeqoutOpenFilename(tmpout, tmpname)) { embExitBad(); } ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta")); ajSeqoutWriteSeq(tmpout, seq); ajSeqoutClose(tmpout); ajSeqoutDel(&tmpout); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); ajStrAssignS(&seqid, ajSeqGetAccS(seq)); if(ajStrGetLen(seqid) == 0) { ajStrAssignS(&seqid, ajSeqGetNameS(seq)); } if(ajStrGetLen(seqid) == 0) { ajWarn("No valid header information\n"); } url = ajStrNew(); ajFmtPrintS(&url, "http://%S/%S/seqinfo/", base, restid); ajFmtPrintF(outf, "Sequence: %S\n", seqid); if(!gFileOutURLS(url, &outf)) { ajDie("Failed to download result from:\n%S\n", url); } ajStrDel(&url); ajStrDel(&restid); ajStrDel(&seqid); ajStrDel(&inseq); } ajFileClose(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&base); embExit(); return 0; }
int main(int argc, char **argv) { EmbPBtreeEntry entry = NULL; AjPStr dbname = NULL; AjPStr dbrs = NULL; AjPStr release = NULL; AjPStr datestr = NULL; AjBool statistics; AjBool compressed; AjPStr directory; AjPStr indexdir; AjPStr filename; AjPStr exclude; AjPStr dbtype = NULL; AjPFile outf = NULL; AjPStr *fieldarray = NULL; ajint nfields; ajint nfiles; AjPStr tmpstr = NULL; AjPStr thysfile = NULL; ajint i; AjPFile inf = NULL; AjPStr word = NULL; AjPBtId idobj = NULL; AjPBtPri priobj = NULL; AjPBtHybrid hyb = NULL; ajulong nentries = 0L; ajulong ientries = 0L; AjPTime starttime = NULL; AjPTime begintime = NULL; AjPTime nowtime = NULL; ajlong startclock = 0; ajlong beginclock = 0; ajlong nowclock = 0; ajulong idcache=0L, idread = 0L, idwrite = 0L, idsize= 0L; ajulong accache=0L, acread = 0L, acwrite = 0L, acsize= 0L; ajulong svcache=0L, svread = 0L, svwrite = 0L, svsize= 0L; ajulong kwcache=0L, kwread = 0L, kwwrite = 0L, kwsize= 0L; ajulong decache=0L, deread = 0L, dewrite = 0L, desize= 0L; ajulong txcache=0L, txread = 0L, txwrite = 0L, txsize= 0L; double tdiff = 0.0; ajint days = 0; ajint hours = 0; ajint mins = 0; embInit("dbxflat", argc, argv); dbtype = ajAcdGetListSingle("idformat"); fieldarray = ajAcdGetList("fields"); directory = ajAcdGetDirectoryName("directory"); outf = ajAcdGetOutfile("outfile"); indexdir = ajAcdGetOutdirName("indexoutdir"); filename = ajAcdGetString("filenames"); exclude = ajAcdGetString("exclude"); dbname = ajAcdGetString("dbname"); dbrs = ajAcdGetString("dbresource"); release = ajAcdGetString("release"); datestr = ajAcdGetString("date"); statistics = ajAcdGetBoolean("statistics"); compressed = ajAcdGetBoolean("compressed"); entry = embBtreeEntryNew(); if(compressed) embBtreeEntrySetCompressed(entry); tmpstr = ajStrNew(); idobj = ajBtreeIdNew(); priobj = ajBtreePriNew(); hyb = ajBtreeHybNew(); nfields = embBtreeSetFields(entry,fieldarray); embBtreeSetDbInfo(entry,dbname,dbrs,datestr,release,dbtype,directory, indexdir); for(i=0; i< nfields; i++) { if(ajStrMatchC(fieldarray[i], "acc")) { accfield = embBtreeGetFieldS(entry, fieldarray[i]); if(compressed) embBtreeFieldSetCompressed(accfield); } else if(ajStrMatchC(fieldarray[i], "sv")) { svfield = embBtreeGetFieldS(entry, fieldarray[i]); if(compressed) embBtreeFieldSetCompressed(svfield); } else if(ajStrMatchC(fieldarray[i], "des")) { desfield = embBtreeGetFieldS(entry, fieldarray[i]); if(compressed) embBtreeFieldSetCompressed(desfield); } else if(ajStrMatchC(fieldarray[i], "key")) { keyfield = embBtreeGetFieldS(entry, fieldarray[i]); if(compressed) embBtreeFieldSetCompressed(keyfield); } else if(ajStrMatchC(fieldarray[i], "org")) { orgfield = embBtreeGetFieldS(entry, fieldarray[i]); if(compressed) embBtreeFieldSetCompressed(orgfield); } else if(!ajStrMatchC(fieldarray[i], "id")) ajErr("Unknown field '%S' specified for indexing", fieldarray[i]); } embBtreeGetRsInfo(entry); nfiles = embBtreeGetFiles(entry,directory,filename,exclude); if(!nfiles) ajDie("No input files in '%S' matched filename '%S'", directory, filename); embBtreeWriteEntryFile(entry); embBtreeOpenCaches(entry); starttime = ajTimeNewToday(); ajFmtPrintF(outf, "Processing directory: %S\n", directory); for(i=0;i<nfiles;++i) { begintime = ajTimeNewToday(); beginclock = ajClockNow(); ajListPop(entry->files,(void **)&thysfile); ajListPushAppend(entry->files,(void *)thysfile); ajFmtPrintS(&tmpstr,"%S%S",entry->directory,thysfile); if(!(inf=ajFileNewInNameS(tmpstr))) ajFatal("Cannot open input file %S\n",tmpstr); ajFilenameTrimPath(&tmpstr); ajFmtPrintF(outf,"Processing file: %S",tmpstr); ientries = 0L; while(dbxflat_NextEntry(entry,inf)) { ++ientries; if(entry->do_id) { if(ajStrGetLen(entry->id) > entry->idlen) { if(ajStrGetLen(entry->id) > maxidlen) { ajWarn("id '%S' too long, truncating to idlen %d", entry->id, entry->idlen); maxidlen = ajStrGetLen(entry->id); } idtrunc++; ajStrKeepRange(&entry->id,0,entry->idlen-1); } ajStrFmtLower(&entry->id); ajStrAssignS(&hyb->key1,entry->id); hyb->dbno = i; hyb->offset = entry->fpos; hyb->dups = 0; ajBtreeHybInsertId(entry->idcache,hyb); ++idtot; } if(accfield) { while(ajListPop(accfield->data,(void **)&word)) { ajStrFmtLower(&word); ajStrAssignS(&hyb->key1,word); hyb->dbno = i; hyb->offset = entry->fpos; hyb->dups = 0; ajBtreeHybInsertId(accfield->cache,hyb); ++acctot; ajStrDel(&word); } } if(svfield) { while(ajListPop(svfield->data,(void **)&word)) { ajStrFmtLower(&word); ajStrAssignS(&hyb->key1,word); hyb->dbno = i; hyb->offset = entry->fpos; hyb->dups = 0; ajBtreeHybInsertId(svfield->cache,hyb); ++svtot; ajStrDel(&word); } } if(keyfield) { while(ajListPop(keyfield->data,(void **)&word)) { ajStrFmtLower(&word); ajStrAssignS(&priobj->id,entry->id); ajStrAssignS(&priobj->keyword,word); priobj->treeblock = 0; ajBtreeInsertKeyword(keyfield->cache, priobj); ++keytot; ajStrDel(&word); } } if(desfield) { while(ajListPop(desfield->data,(void **)&word)) { ajStrFmtLower(&word); ajStrAssignS(&priobj->id,entry->id); ajStrAssignS(&priobj->keyword,word); priobj->treeblock = 0; if(ajBtreeInsertKeyword(desfield->cache, priobj)) ++destot; ajStrDel(&word); } } if(orgfield) { while(ajListPop(orgfield->data,(void **)&word)) { ajStrFmtLower(&word); ajStrAssignS(&priobj->id,entry->id); ajStrAssignS(&priobj->keyword,word); priobj->treeblock = 0; ajBtreeInsertKeyword(orgfield->cache, priobj); ++orgtot; ajStrDel(&word); } } } ajFileClose(&inf); nentries += ientries; nowtime = ajTimeNewToday(); nowclock = ajClockNow(); ajFmtPrintF(outf, " entries: %Lu (%Lu) time: %.1f/%.1fs (%.1f/%.1fs)\n", nentries, ientries, ajClockDiff(startclock,nowclock), ajTimeDiff(starttime, nowtime), ajClockDiff(beginclock,nowclock), ajTimeDiff(begintime, nowtime)); if(statistics) { if(entry->do_id) ajBtreeCacheStatsOut(outf, entry->idcache, &idcache, &idread, &idwrite, &idsize); if(accfield) ajBtreeCacheStatsOut(outf, accfield->cache, &accache, &acread, &acwrite, &acsize); if(svfield) ajBtreeCacheStatsOut(outf, svfield->cache, &svcache, &svread, &svwrite, &svsize); if(keyfield) ajBtreeCacheStatsOut(outf, keyfield->cache, &kwcache, &kwread, &kwwrite, &kwsize); if(desfield) ajBtreeCacheStatsOut(outf, desfield->cache, &decache, &deread, &dewrite, &desize); if(orgfield) ajBtreeCacheStatsOut(outf, orgfield->cache, &txcache, &txread, &txwrite, &txsize); } ajTimeDel(&begintime); ajTimeDel(&nowtime); } embBtreeDumpParameters(entry); embBtreeCloseCaches(entry); nowtime = ajTimeNewToday(); tdiff = ajTimeDiff(starttime, nowtime); days = (ajint) (tdiff/(24.0*3600.0)); tdiff -= (24.0*3600.0)*(double)days; hours = (ajint) (tdiff/3600.0); tdiff -= 3600.0*(double)hours; mins = (ajint) (tdiff/60.0); tdiff -= 60.0 * (double) mins; if(days) ajFmtPrintF(outf, "Total time: %d %02d:%02d:%04.1f\n", days, hours, mins, tdiff); else if (hours) ajFmtPrintF(outf, "Total time: %d:%02d:%04.1f\n", hours, mins, tdiff); else ajFmtPrintF(outf, "Total time: %d:%04.1f\n", mins, tdiff); ajTimeDel(&nowtime); ajTimeDel(&starttime); if(maxidlen) { ajFmtPrintF(outf, "Resource idlen truncated %u IDs. " "Maximum ID length was %u.", idtrunc, maxidlen); ajWarn("Resource idlen truncated %u IDs. Maximum ID length was %u.", idtrunc, maxidlen); } ajFileClose(&outf); embBtreeEntryDel(&entry); ajStrDel(&tmpstr); ajStrDel(&filename); ajStrDel(&exclude); ajStrDel(&dbname); ajStrDel(&dbrs); ajStrDel(&release); ajStrDel(&datestr); ajStrDel(&directory); ajStrDel(&indexdir); ajStrDel(&dbtype); nfields = 0; while(fieldarray[nfields]) ajStrDel(&fieldarray[nfields++]); AJFREE(fieldarray); ajBtreeIdDel(&idobj); ajBtreePriDel(&priobj); ajBtreeHybDel(&hyb); ajRegFree(&dbxflat_wrdexp); embExit(); return 0; }
int main(int argc, char **argv) { /* Variable declarations */ AjPOutfile outfile = NULL; AjBool obsolete = ajTrue; AjPObo obo = NULL; AjPObo oboanc = NULL; AjPObo oboparent = NULL; AjPOboall oboall = NULL; AjPOboin oboin = NULL; AjPStr oboqryup = NULL; AjPStr oboqryanc = NULL; AjPTable alltable = NULL; AjPTable newtable = NULL; AjPStr up = NULL; AjPList uplist = NULL; ajuint iterms = 0; AjPStr topid = NULL; AjPStr obodb = NULL; AjBool saved = ajFalse; /* ACD processing */ embInit("ontogetcommon", argc, argv); oboall = ajAcdGetOboall("oboterms"); outfile = ajAcdGetOutobo("outfile"); obsolete = ajAcdGetBoolean("obsolete"); oboin = ajOboinNew(); oboparent = ajOboNew(); oboanc = ajOboNew(); uplist = ajListNew(); alltable = ajTablestrNew(600); newtable = ajTablestrNew(600); while(ajOboallNext(oboall, &obo)) { saved = ajFalse; if(!obsolete && ajOboIsObsolete(obo)) continue; if(!iterms) { ajDebug("store id '%S'\n", ajOboGetId(obo)); ajStrAssignS(&obodb, ajOboGetDb(obo)); ajTablePut(alltable, ajStrNewS(ajOboGetId(obo)), NULL); saved = ajTrue; } else { ajDebug("test id '%S'\n", ajOboGetId(obo)); if(ajTableMatchS(alltable, ajOboGetId(obo))) { ajDebug("keep id '%S'\n", ajOboGetId(obo)); ajTablePut(newtable, ajStrNewS(ajOboGetId(obo)), NULL); saved = ajTrue; } } if(saved) ajStrAssignS(&topid, ajOboGetId(obo)); if(ajOboGetParents(obo, uplist)) /* that was the root */ { while(ajListstrPop(uplist, &up)) { ajDebug("up: '%S'\n", up); ajFmtPrintS(&oboqryup, "%S-id:%S", ajOboGetDb(obo), up); ajOboinQryS(oboin, oboqryup); while(ajOboinRead(oboin, oboparent)) { if(!obsolete && ajOboIsObsolete(oboparent)) continue; if(!iterms) { ajDebug("store parent '%S'\n", ajOboGetId(oboparent)); ajTablePut(alltable, ajStrNewS(ajOboGetId(oboparent)), NULL); } else { ajDebug("test parent '%S'\n", ajOboGetId(oboparent)); if(ajTableMatchS(alltable, ajOboGetId(oboparent))) { ajDebug("keep parent '%S'\n", ajOboGetId(oboparent)); ajTablePut(newtable, ajStrNewS(ajOboGetId(oboparent)), NULL); if(!saved) { ajStrAssignS(&topid, ajOboGetId(oboparent)); saved = ajTrue; } } } if(!ajOboGetParents(oboparent, uplist)) continue; } ajStrDel(&up); } } if(iterms) ajTableMergeAnd(alltable, newtable); ajDebug("id: '%S' saved %u\n", ajOboGetId(obo), ajTableGetLength(alltable)); if(!ajTableGetLength(alltable)) ajDie("Query '%S' no matching ancestor found for obo term '%S:%S'", ajOboallGetQryS(oboall), ajOboGetDb(obo), ajOboGetId(obo)); iterms++; } ajFmtPrintS(&oboqryanc, "%S-id:%S", obodb, topid); ajOboinQryS(oboin, oboqryanc); while(ajOboinRead(oboin, oboanc)) { ajObooutWrite(outfile, oboanc); } /* Memory clean-up and exit */ ajOboallDel(&oboall); ajOboinDel(&oboin); ajOboDel(&oboanc); ajOboDel(&oboparent); ajListFree(&uplist); ajTablestrFreeKey(&alltable); ajTablestrFreeKey(&newtable); ajStrDel(&oboqryup); ajStrDel(&oboqryanc); ajStrDel(&obodb); ajStrDel(&topid); ajOutfileClose(&outfile); embExit(); return 0; }
int main(int argc, char **argv) { AjPList idlist; AjPList* fieldList = NULL; AjBool systemsort; AjBool cleanup; ajuint maxindex; ajuint maxidlen = 0; ajuint maxlen; AjPFile elistfile = NULL; AjPFile* alistfile = NULL; AjPStr dbname = NULL; AjPStr release = NULL; AjPStr datestr = NULL; AjPStr sortopt = NULL; void **entryIds = NULL; AjPStr directory; AjPStr indexdir; AjPStr filename; AjPStr exclude; AjPStr curfilename = NULL; AjPFile libr=NULL; AjPStr idformat = NULL; EmbPEntry entry; ajuint idtype = 0; ajuint idCount = 0; ajuint idDone; AjPList listInputFiles = NULL; void ** inputFiles = NULL; ajuint nfiles; ajuint ifile; ajuint filesize; short recsize; ajuint maxfilelen = 20; char date[4] = { 0,0,0,0 }; AjPStr tmpfname = NULL; AjPStr* fields = NULL; AjPFile entFile = NULL; AjPStr* divfiles = NULL; AjPRegexp regIdExp = NULL; ajint* maxFieldLen = NULL; ajuint ifield = 0; ajuint nfields = 0; AjPFile logfile = NULL; ajuint* countField = NULL; ajuint* fieldTot = NULL; ajuint idCountFile = 0; ajuint i; embInit("dbifasta", argc, argv); idformat = ajAcdGetListSingle("idformat"); fields = ajAcdGetList("fields"); directory = ajAcdGetDirectoryName("directory"); indexdir = ajAcdGetOutdirName("indexoutdir"); filename = ajAcdGetString("filenames"); exclude = ajAcdGetString("exclude"); dbname = ajAcdGetString("dbname"); release = ajAcdGetString("release"); datestr = ajAcdGetString("date"); systemsort = ajAcdGetBoolean("systemsort"); cleanup = ajAcdGetBoolean("cleanup"); sortopt = ajAcdGetString("sortoptions"); maxindex = ajAcdGetInt("maxindex"); logfile = ajAcdGetOutfile("outfile"); while(fields[nfields]) /* array ends with a NULL */ nfields++; if(nfields) { AJCNEW(maxFieldLen, nfields); AJCNEW0(countField, nfields); AJCNEW0(fieldTot, nfields); for(ifield=0; ifield < nfields; ifield++) maxFieldLen[ifield] = (ajint)maxindex * -1; if(systemsort) AJCNEW(alistfile, nfields); else { AJCNEW(fieldList, nfields); for(ifield=0; ifield < nfields; ifield++) fieldList[ifield] = ajListNew(); } } if(ajStrMatchC(datestr, "00/00/00")) ajFmtPrintS(&datestr, "%D", ajTimeRefTodayFmt("dbindex")); ajStrRemoveWhite(&dbname); /* used for temp filenames */ embDbiDateSet(datestr, date); idlist = ajListNew(); regIdExp = dbifasta_getExpr(idformat, &idtype); ajDebug("reading '%S/%S'\n", directory, filename); ajDebug("writing '%S/'\n", indexdir); listInputFiles = embDbiFileListExc(directory, filename, exclude); ajListSort(listInputFiles, &ajStrVcmp); nfiles = (ajuint) ajListToarray(listInputFiles, &inputFiles); if(!nfiles) ajDie("No input files in '%S' matched filename '%S'", directory, filename); embDbiLogHeader(logfile, dbname, release, datestr, indexdir, maxindex); embDbiLogFields(logfile, fields, nfields); embDbiLogSource(logfile, directory, filename, exclude, (AjPStr*) inputFiles, nfiles); embDbiLogCmdline(logfile); AJCNEW0(divfiles, nfiles); /* ** process each input file, one at a time */ for(ifile=0; ifile < nfiles; ifile++) { ajStrAssignS(&curfilename,(AjPStr) inputFiles[ifile]); embDbiFlatOpenlib(curfilename, &libr); ajFilenameTrimPath(&curfilename); if(ajStrGetLen(curfilename) >= maxfilelen) maxfilelen = ajStrGetLen(curfilename) + 1; ajDebug("processing filename '%S' ...\n", curfilename); ajDebug("processing file '%F' ...\n", libr); ajStrAssignS(&divfiles[ifile], curfilename); if(systemsort) /* elistfile for entries, alist for fields */ elistfile = embDbiSortOpen(alistfile, ifile, dbname, fields, nfields); idCountFile = 0; for(i=0;i<nfields;i++) countField[i] = 0; while((entry=dbifasta_NextFlatEntry(libr, ifile, regIdExp, idtype, systemsort, fields, maxFieldLen, &maxidlen, countField, elistfile, alistfile))) { idCountFile++; if(!systemsort) /* save the entry data in lists */ embDbiMemEntry(idlist, fieldList, nfields, entry, ifile); entry = NULL; } idCount += idCountFile; if(systemsort) { embDbiSortClose(&elistfile, alistfile, nfields); AJFREE(entry); } else { embDbiEntryDel(&dbifastaGEntry); } embDbiLogFile(logfile, curfilename, idCountFile, fields, countField, nfields); } /* write the division.lkp file */ embDbiWriteDivision(indexdir, dbname, release, date, maxfilelen, nfiles, divfiles, NULL); /* Write the entryname.idx index */ ajStrAssignC(&tmpfname, "entrynam.idx"); entFile = ajFileNewOutNamePathS(tmpfname, indexdir); recsize = maxidlen+10; filesize = 300 + (idCount*(ajint)recsize); embDbiHeader(entFile, filesize, idCount, recsize, dbname, release, date); if(systemsort) idDone = embDbiSortWriteEntry(entFile, maxidlen, dbname, nfiles, cleanup, sortopt); else /* save entries in entryIds array */ { idDone = embDbiMemWriteEntry(entFile, maxidlen, idlist, &entryIds); if(idDone != idCount) ajFatal("Duplicates not allowed for in-memory processing"); } embDbiHeaderSize(entFile, 300+(idDone*(ajint)recsize), idDone); ajFileClose(&entFile); /* Write the fields index files */ for(ifield=0; ifield < nfields; ifield++) { if(maxindex) maxlen = maxindex; else { if(maxFieldLen[ifield] >= 0) maxlen = maxFieldLen[ifield]; else maxlen = - maxFieldLen[ifield]; } if(systemsort) fieldTot[ifield] = embDbiSortWriteFields(dbname, release, date, indexdir, fields[ifield], maxlen, nfiles, idCount, cleanup, sortopt); else fieldTot[ifield] = embDbiMemWriteFields(dbname, release, date, indexdir, fields[ifield], maxlen, fieldList[ifield], entryIds); } embDbiLogFinal(logfile,maxindex, maxFieldLen, fields, fieldTot, nfields, nfiles, idDone, idCount); if(systemsort) embDbiRmEntryFile(dbname, cleanup); ajStrDel(&idformat); ajStrDelarray(&fields); ajStrDel(&filename); ajStrDel(&exclude); ajStrDel(&dbname); ajStrDel(&release); ajStrDel(&datestr); ajStrDel(&sortopt); ajStrDel(&directory); ajStrDel(&indexdir); ajStrDel(&tmpfname); ajFileClose(&libr); ajFileClose(&logfile); for(i=0;i<nfields;i++) { if(systemsort) { ajFileClose(&alistfile[i]); } else { ajListMap(fieldList[i], &embDbiFieldDelMap, NULL); ajListFree(&fieldList[i]); } } AJFREE(alistfile); AJFREE(fieldList); AJFREE(maxFieldLen); AJFREE(countField); AJFREE(fieldTot); for(i=0;i<nfiles;i++) { ajStrDel(&divfiles[i]); } AJFREE(divfiles); AJFREE(inputFiles); embDbiEntryDel(&dbifastaGEntry); ajStrDel(&dbifastaGRline); ajStrDel(&dbifastaGTmpId); if(dbifastaGFdl) { for(i=0; i < nfields; i++) ajListFree(&dbifastaGFdl[i]); AJFREE(dbifastaGFdl); } ajListMap(idlist, &embDbiEntryDelMap, NULL); ajListFree(&idlist); ajListstrFreeData(&listInputFiles); AJFREE(entryIds); ajRegFree(&dbifastaGIdexp); ajRegFree(&dbifastaGWrdexp); ajRegFree(®IdExp); ajStrDel(&dbifastaGTmpAc); ajStrDel(&dbifastaGTmpSv); ajStrDel(&dbifastaGTmpGi); ajStrDel(&dbifastaGTmpDb); ajStrDel(&dbifastaGTmpDes); ajStrDel(&dbifastaGTmpFd); ajStrDel(&curfilename); embExit(); return 0; }
int main(int argc, char **argv) { AjPAlign align; AjPSeqall seqall; AjPSeq a; AjPSeq b; AjPStr alga; AjPStr algb; AjPStr ss; ajuint lena; ajuint lenb; const char *p; const char *q; ajint start1 = 0; ajint start2 = 0; float *path; ajint *compass; float* ix; float* iy; float* m; AjPMatrixf matrix; AjPSeqCvt cvt = 0; float **sub; float gapopen; float gapextend; float endgapopen; float endgapextend; ajulong maxarr = 1000; /* arbitrary. realloc'd if needed */ ajulong len; float score; AjBool dobrief = ajTrue; AjBool endweight = ajFalse; /* whether end gap penalties should be applied */ float id = 0.; float sim = 0.; float idx = 0.; float simx = 0.; AjPStr tmpstr = NULL; size_t stlen; embInit("needle", argc, argv); matrix = ajAcdGetMatrixf("datafile"); a = ajAcdGetSeq("asequence"); ajSeqTrim(a); seqall = ajAcdGetSeqall("bsequence"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); endgapopen = ajAcdGetFloat("endopen"); endgapextend = ajAcdGetFloat("endextend"); dobrief = ajAcdGetBoolean("brief"); endweight = ajAcdGetBoolean("endweight"); align = ajAcdGetAlign("outfile"); gapopen = ajRoundFloat(gapopen, 8); gapextend = ajRoundFloat(gapextend, 8); AJCNEW(path, maxarr); AJCNEW(compass, maxarr); AJCNEW(m, maxarr); AJCNEW(ix, maxarr); AJCNEW(iy, maxarr); alga = ajStrNew(); algb = ajStrNew(); ss = ajStrNew(); sub = ajMatrixfGetMatrix(matrix); cvt = ajMatrixfGetCvt(matrix); lena = ajSeqGetLen(a); while(ajSeqallNext(seqall,&b)) { ajSeqTrim(b); lenb = ajSeqGetLen(b); if(lenb > (ULONG_MAX/(ajulong)(lena+1))) ajFatal("Sequences too big. Try 'stretcher' or 'supermatcher'"); len = lena*lenb; if(len>maxarr) { stlen = (size_t) len; AJCRESIZETRY(path,stlen); if(!path) ajDie("Sequences too big. Try 'stretcher'"); AJCRESIZETRY(compass,stlen); if(!compass) ajDie("Sequences too big. Try 'stretcher'"); AJCRESIZETRY(m,stlen); if(!m) ajDie("Sequences too big. Try 'stretcher'"); AJCRESIZETRY(ix,stlen); if(!ix) ajDie("Sequences too big. Try 'stretcher'"); AJCRESIZETRY(iy,stlen); if(!iy) ajDie("Sequences too big. Try 'stretcher'"); maxarr=len; } p = ajSeqGetSeqC(a); q = ajSeqGetSeqC(b); ajStrAssignC(&alga,""); ajStrAssignC(&algb,""); score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb, gapopen, gapextend, endgapopen, endgapextend, &start1, &start2, path, sub, cvt, m, ix, iy, compass, ajTrue, endweight); embAlignWalkNWMatrixUsingCompass(p, q, &alga, &algb, lena, lenb, &start1, &start2, compass); embAlignReportGlobal(align, a, b, alga, algb, start1, start2, gapopen, gapextend, score, matrix, ajSeqGetOffset(a), ajSeqGetOffset(b)); if(!dobrief) { embAlignCalcSimilarity(alga,algb,sub,cvt,lena,lenb,&id,&sim,&idx, &simx); ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n", id); ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n", sim); ajFmtPrintAppS(&tmpstr,"Shortest_Identity = %5.2f%%\n", idx); ajFmtPrintAppS(&tmpstr,"Shortest_Similarity = %5.2f%%", simx); ajAlignSetSubHeaderApp(align, tmpstr); } ajAlignWrite(align); ajAlignReset(align); } ajAlignClose(align); ajAlignDel(&align); ajSeqallDel(&seqall); ajSeqDel(&a); ajSeqDel(&b); AJFREE(compass); AJFREE(path); AJFREE(ix); AJFREE(iy); AJFREE(m); ajStrDel(&alga); ajStrDel(&algb); ajStrDel(&ss); ajStrDel(&tmpstr); embExit(); return 0; }
int main(int argc, char *argv[]) { embInitPV("gbasezvalue", argc, argv, "GEMBASSY", "1.0.3"); AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; AjPStr position = NULL; ajint limit = 0; ajint PatLen = 0; ajint upstream = 0; ajint downstream = 0; AjBool accid = ajFalse; AjPStr restid = NULL; AjPStr seqid = NULL; AjPStr base = NULL; AjPStr url = NULL; AjPFile tmpfile = NULL; AjPStr tmpname = NULL; AjPFile outf = NULL; seqall = ajAcdGetSeqall("sequence"); position = ajAcdGetSelectSingle("position"); limit = ajAcdGetInt("limit"); PatLen = ajAcdGetInt("patlen"); upstream = ajAcdGetInt("upstream"); downstream = ajAcdGetInt("downstream"); accid = ajAcdGetBoolean("accid"); outf = ajAcdGetOutfile("outfile"); base = ajStrNewC("rest.g-language.org"); gAssignUniqueName(&tmpname); while(ajSeqallNext(seqall, &seq)) { inseq = NULL; if(!accid) { if(gFormatGenbank(seq, &inseq)) { tmpfile = ajFileNewOutNameS(tmpname); if(!tmpfile) { ajDie("Output file (%S) open error\n", tmpname); } ajFmtPrintF(tmpfile, "%S", inseq); ajFileClose(&tmpfile); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); } else { ajWarn("Sequence does not have features\n" "Proceeding with sequence accession ID\n"); accid = ajTrue; } } ajStrAssignS(&seqid, ajSeqGetAccS(seq)); if(ajStrGetLen(seqid) == 0) { ajStrAssignS(&seqid, ajSeqGetNameS(seq)); } if(ajStrGetLen(seqid) == 0) { ajWarn("No valid header information\n"); } if(accid) { ajStrAssignS(&restid, seqid); if(ajStrGetLen(seqid) == 0) { ajDie("Cannot proceed without header with -accid\n"); } if(!gValID(seqid)) { ajDie("Invalid accession ID:%S, exiting\n", seqid); } } url = ajStrNew(); ajFmtPrintS(&url, "http://%S/%S/base_z_value/position=%S/PatLen=%d" "upstream=%d/downstream=%d/limit=%d/output=f/tag=gene", base, restid, position, PatLen, upstream, downstream, limit); ajFmtPrintF(outf, "Sequence: %S\n", seqid); if(!gFileOutURLS(url, &outf)) { ajDie("Failed to download result from:\n%S\n", url); } ajStrDel(&url); ajStrDel(&restid); ajStrDel(&seqid); ajStrDel(&inseq); } ajFileClose(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&base); ajStrDel(&position); embExit(); return 0; }
int main(int argc, char *argv[]) { embInitPV("ggcskew", argc, argv, "GEMBASSY", "1.0.3"); AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; AjBool accid = ajFalse; AjPStr restid = NULL; AjPStr seqid = NULL; AjPStr base = NULL; AjPStr url = NULL; AjPStr tmpname = NULL; AjPSeqout tmpout = NULL; ajint window = 0; ajint slide = 0; AjBool cumulative = 0; AjBool at = 0; AjBool purine = 0; AjBool keto = 0; AjBool plot = 0; AjPFile outf = NULL; AjPFilebuff buff = NULL; AjPGraph mult = NULL; gPlotParams gpp; AjPStr title = NULL; seqall = ajAcdGetSeqall("sequence"); window = ajAcdGetInt("window"); slide = ajAcdGetInt("slide"); cumulative = ajAcdGetBoolean("cumulative"); at = ajAcdGetBoolean("at"); purine = ajAcdGetBoolean("purine"); keto = ajAcdGetBoolean("keto"); plot = ajAcdGetToggle("plot"); outf = ajAcdGetOutfile("outfile"); mult = ajAcdGetGraphxy("graph"); base = ajStrNewC("rest.g-language.org"); gAssignUniqueName(&tmpname); ajStrAppendC(&tmpname, ".fasta"); while(ajSeqallNext(seqall, &seq)) { tmpout = ajSeqoutNew(); if(!ajSeqoutOpenFilename(tmpout, tmpname)) { embExitBad(); } ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta")); ajSeqoutWriteSeq(tmpout, seq); ajSeqoutClose(tmpout); ajSeqoutDel(&tmpout); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); ajStrAssignS(&seqid, ajSeqGetAccS(seq)); if(ajStrGetLen(seqid) == 0) { ajStrAssignS(&seqid, ajSeqGetNameS(seq)); } if(ajStrGetLen(seqid) == 0) { ajWarn("No valid header information\n"); } url = ajStrNew(); ajFmtPrintS(&url, "http://%S/%S/gcskew/window=%d/slide=%d/cumulative=%d/" "at=%d/purine=%d/keto=%d/output=f/", base, restid, window, slide, cumulative, at, purine, keto); if(plot) { title = ajStrNew(); ajStrAppendC(&title, argv[0]); ajStrAppendC(&title, " of "); ajStrAppendS(&title, seqid); gpp.title = ajStrNewS(title); gpp.xlab = ajStrNewC("location"); gpp.ylab = ajStrNewC("GC skew"); if(!gFilebuffURLS(url, &buff)) { ajDie("File downloading error from:\n%S\n", url); } if(!gPlotFilebuff(buff, mult, &gpp)) { ajDie("Error in plotting\n"); } AJFREE(gpp.title); AJFREE(gpp.xlab); AJFREE(gpp.ylab); ajStrDel(&title); ajFilebuffDel(&buff); } else { ajFmtPrintF(outf, "Sequence: %S\n", seqid); if(!gFileOutURLS(url, &outf)) { ajDie("File downloading error from:\n%S\n", url); } } ajStrDel(&url); ajStrDel(&restid); ajStrDel(&seqid); } ajFileClose(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&base); embExit(); return 0; }
int main(int argc, char **argv) { AjPList idlist; AjPList* fieldList = NULL; AjBool systemsort; AjBool cleanup; ajint blastv = 0; char dbtype = '\0'; ajuint maxindex; ajuint maxidlen = 0; ajuint maxlen; AjPStr version = NULL; AjPStr seqtype = NULL; AjPFile elistfile = NULL; AjPFile* alistfile = NULL; AjPStr dbname = NULL; AjPStr release = NULL; AjPStr datestr = NULL; AjPStr sortopt = NULL; void **entryIds = NULL; AjBool usesrc = AJTRUE; AjPStr directory; AjPStr indexdir; AjPStr filename; AjPStr exclude; AjPStr curfilename = NULL; AjPStr idformat = NULL; EmbPEntry entry; PBlastDb db = NULL; ajuint idCount = 0; ajuint idDone; AjPList listTestFiles = NULL; void ** testFiles = NULL; ajuint nfiles; ajuint ifile; ajuint jfile; ajuint filesize; short recsize; ajuint maxfilelen = 20; char date[4] = { 0,0,0,0 }; AjPStr tmpfname = NULL; AjPStr* fields = NULL; AjPFile entFile = NULL; AjPStr* divfiles = NULL; ajint* maxFieldLen = NULL; ajuint ifield = 0; ajuint nfields = 0; AjPFile logfile = NULL; ajuint* countField = NULL; ajuint* fieldTot = NULL; ajuint idCountFile = 0; ajuint i = 0; embInit("dbiblast", argc, argv); idformat = ajStrNewC("NCBI"); fields = ajAcdGetList("fields"); directory = ajAcdGetDirectoryName("directory"); indexdir = ajAcdGetOutdirName("indexoutdir"); filename = ajAcdGetString("filenames"); exclude = ajAcdGetString("exclude"); dbname = ajAcdGetString("dbname"); release = ajAcdGetString("release"); datestr = ajAcdGetString("date"); systemsort = ajAcdGetBoolean("systemsort"); cleanup = ajAcdGetBoolean("cleanup"); sortopt = ajAcdGetString("sortoptions"); maxindex = ajAcdGetInt("maxindex"); version = ajAcdGetListSingle("blastversion"); seqtype = ajAcdGetListSingle("seqtype"); usesrc = ajAcdGetBoolean("sourcefile"); logfile = ajAcdGetOutfile("outfile"); while(fields[nfields]) /* array ends with a NULL */ nfields++; if(nfields) { AJCNEW(maxFieldLen, nfields); AJCNEW0(countField, nfields); AJCNEW0(fieldTot, nfields); for(ifield=0; ifield < nfields; ifield++) maxFieldLen[ifield] = (ajint) maxindex * -1; if(systemsort) AJCNEW(alistfile, nfields); else { AJCNEW(fieldList, nfields); for(ifield=0; ifield < nfields; ifield++) fieldList[ifield] = ajListNew(); } } if(ajStrMatchC(datestr, "00/00/00")) ajFmtPrintS(&datestr, "%D", ajTimeRefTodayFmt("dbindex")); ajStrRemoveWhite(&dbname); /* used for temp filenames */ embDbiDateSet(datestr, date); idlist = ajListNew(); if(ajUtilGetBigendian()) readReverse = ajFalse; else readReverse = ajTrue; ajStrToInt(version, &blastv); dbtype = ajStrGetCharFirst(seqtype); ajDebug("reading '%S/%S'\n", directory, filename); ajDebug("writing '%S/'\n", indexdir); listTestFiles = embDbiFileListExc(directory, filename, exclude); ajListSort(listTestFiles, ajStrVcmp); nfiles = ajListToarray(listTestFiles, &testFiles); if(!nfiles) ajDie("No input files in '%S' matched filename '%S'", directory, filename); embDbiLogHeader(logfile, dbname, release, datestr, indexdir, maxindex); embDbiLogFields(logfile, fields, nfields); embDbiLogSource(logfile, directory, filename, exclude, (AjPStr*) testFiles, nfiles); embDbiLogCmdline(logfile); AJCNEW0(divfiles, nfiles); /* ** process each input file, one at a time */ jfile = 0; for(ifile=0; ifile < nfiles; ifile++) { curfilename = (AjPStr) testFiles[ifile]; if(!dbiblast_blastopenlib(curfilename, usesrc, blastv, dbtype, &db)) continue; /* could be the wrong file type with "*.*" */ ajDebug("processing filename '%S' ...\n", curfilename); ajDebug("processing file '%S' ...\n", db->TFile->Name); ajStrAssignS(&divfiles[jfile], db->TFile->Name); ajFilenameTrimPath(&divfiles[jfile]); if(ajStrGetLen(divfiles[jfile]) >= maxfilelen) maxfilelen = ajStrGetLen(divfiles[jfile]) + 1; if(systemsort) /* elistfile for entries, alist for fields */ elistfile = embDbiSortOpen(alistfile, jfile, dbname, fields, nfields); idCountFile = 0; for(i=0;i<nfields;i++) countField[i] = 0; while((entry=dbiblast_nextblastentry(db, jfile, idformat, systemsort, fields, maxFieldLen, &maxidlen, countField, elistfile, alistfile))) { idCountFile++; if(!systemsort) /* save the entry data in lists */ { embDbiMemEntry(idlist, fieldList, nfields, entry, jfile); } } idCount += idCountFile; if(systemsort) { embDbiSortClose(&elistfile, alistfile, nfields); /* lost the entry, so can't free it :-) */ } embDbiLogFile(logfile, curfilename, idCountFile, fields, countField, nfields); dbiblast_dbfree(&db); jfile++; } nfiles = jfile; /* ** write the division.lkp file */ embDbiWriteDivision(indexdir, dbname, release, date, maxfilelen, nfiles, divfiles, NULL); /* ** Write the entryname.idx index */ ajStrAssignC(&tmpfname, "entrynam.idx"); entFile = ajFileNewOutNamePathS(tmpfname, indexdir); recsize = maxidlen+10; filesize = 300 + (idCount*(ajint)recsize); embDbiHeader(entFile, filesize, idCount, recsize, dbname, release, date); if(systemsort) idDone = embDbiSortWriteEntry(entFile, maxidlen, dbname, nfiles, cleanup, sortopt); else /* save entries in entryIds array */ { idDone = embDbiMemWriteEntry(entFile, maxidlen, idlist, &entryIds); if(idDone != idCount) ajFatal("Duplicates not allowed for in-memory processing"); } embDbiHeaderSize(entFile, 300+(idDone*(ajint)recsize), idDone); ajFileClose(&entFile); /* ** Write the fields index files */ for(ifield=0; ifield < nfields; ifield++) { if(maxindex) maxlen = maxindex; else { if(maxFieldLen[ifield] >= 0) maxlen = maxFieldLen[ifield]; else maxlen = - maxFieldLen[ifield]; } if(systemsort) fieldTot[ifield] = embDbiSortWriteFields(dbname, release, date, indexdir, fields[ifield], maxlen, nfiles, idCount, cleanup, sortopt); else fieldTot[ifield] = embDbiMemWriteFields(dbname, release, date, indexdir, fields[ifield], maxlen, fieldList[ifield], entryIds); } embDbiLogFinal(logfile,maxindex, maxFieldLen, fields, fieldTot, nfields, nfiles, idDone, idCount); if(systemsort) embDbiRmEntryFile(dbname, cleanup); ajListMap(idlist, embDbiEntryDelMap, NULL); ajListFree(&idlist); AJFREE(entryIds); ajStrDelarray(&fields); for(i=0;i<nfields;i++) { if(systemsort) { ajFileClose(&alistfile[i]); } else { ajListMap(fieldList[i], embDbiFieldDelMap, NULL); ajListFree(&fieldList[i]); } } AJFREE(alistfile); AJFREE(fieldList); ajStrDel(&version); ajStrDel(&seqtype); ajFileClose(&elistfile); for(i=0;i<nfiles;i++) { ajStrDel(&divfiles[i]); } AJFREE(countField); AJFREE(fieldTot); ajStrDel(&dbname); ajStrDel(&release); ajStrDel(&datestr); ajStrDel(&sortopt); ajStrDel(&directory); ajStrDel(&indexdir); ajStrDel(&filename); ajStrDel(&exclude); ajStrDel(&idformat); ajStrDel(&tmpfname); AJFREE(maxFieldLen); ajFileClose(&logfile); ajListstrFreeData(&listTestFiles); ajStrDel(&t); ajStrDel(&id); ajStrDel(&acc); ajStrDel(&hline); ajStrDel(&tmpdes); ajStrDel(&tmpfd); ajStrDel(&tmpgi); ajStrDel(&tmpdb); ajStrDel(&tmpac); ajStrDel(&tmpsv); ajRegFree(&wrdexp); embDbiEntryDel(&dbiblastEntry); if(fdl) { for(i=0; i < nfields; i++) ajListFree(&fdl[i]); AJFREE(fdl); } for(i=0;i<nfiles;i++) { ajStrDel(&divfiles[i]); } AJFREE(divfiles); AJFREE(testFiles); 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("gviewcds", argc, argv, "GEMBASSY", "1.0.1"); AjPSeqall seqall; AjPSeq seq; AjPStr inseq = NULL; ajint length = 0; ajint gap = 0; AjBool accid = ajFalse; AjPStr restid = NULL; AjPStr seqid = NULL; AjPStr base = NULL; AjPStr url = NULL; AjPFile tmpfile = NULL; AjPStr tmpname = NULL; AjBool plot = 0; AjPFile outf = NULL; AjPFilebuff buff = NULL; AjPGraph mult = NULL; gPlotParams gpp; AjPStr title = NULL; AjPPStr names = NULL; ajint i; seqall = ajAcdGetSeqall("sequence"); length = ajAcdGetInt("length"); gap = ajAcdGetInt("gap"); accid = ajAcdGetBoolean("accid"); plot = ajAcdGetToggle("plot"); outf = ajAcdGetOutfile("outfile"); mult = ajAcdGetGraphxy("graph"); base = ajStrNewC("rest.g-language.org"); gAssignUniqueName(&tmpname); while(ajSeqallNext(seqall, &seq)) { inseq = NULL; if(!accid) { if(gFormatGenbank(seq, &inseq)) { gAssignUniqueName(&tmpname); tmpfile = ajFileNewOutNameS(tmpname); if(!tmpfile) { ajFmtError("Output file (%S) open error\n", tmpname); embExitBad(); } ajFmtPrintF(tmpfile, "%S", inseq); ajFileClose(&tmpfile); ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); gFilePostSS(url, tmpname, &restid); ajStrDel(&url); ajSysFileUnlinkS(tmpname); } else { ajFmtError("Sequence does not have features\n" "Proceeding with sequence accession ID\n"); accid = ajTrue; } } if(accid) { ajStrAssignS(&seqid, ajSeqGetAccS(seq)); if(!ajStrGetLen(seqid)) { ajStrAssignS(&seqid, ajSeqGetNameS(seq)); } if(!ajStrGetLen(seqid)) { ajFmtError("No valid header information\n"); embExitBad(); } ajStrAssignS(&restid, seqid); } ajStrAssignS(&seqid, ajSeqGetAccS(seq)); url = ajStrNew(); ajFmtPrintS(&url, "http://%S/%S/view_cds/length=%d/gap=%d/" "output=f/tag=gene", base, restid, length, gap); if(plot) { if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) { ajDie("Error in memory allocation, exiting\n"); } names[0] = NULL; names[1] = ajStrNewC("A"); names[2] = ajStrNewC("T"); names[3] = ajStrNewC("G"); names[4] = ajStrNewC("C"); title = ajStrNew(); ajStrAppendC(&title, argv[0]); ajStrAppendC(&title, " of "); ajStrAppendS(&title, seqid); gpp.title = ajStrNewS(title); gpp.xlab = ajStrNewC("position"); gpp.ylab = ajStrNewC("percentage"); gpp.names = names; if(!gFilebuffURLS(url, &buff)) { ajDie("File downloading error from:\n%S\n", url); } if(!gPlotFilebuff(buff, mult, &gpp)) { ajDie("Error in plotting\n"); } i = 0; while(names[i]) { AJFREE(names[i]); ++i; } AJFREE(names); AJFREE(gpp.title); AJFREE(gpp.xlab); AJFREE(gpp.ylab); ajStrDel(&title); ajFilebuffDel(&buff); } else { ajFmtPrintF(outf, "Sequence: %S\n", seqid); if(!gFileOutURLS(url, &outf)) { ajDie("File downloading error from:\n%S\n", url); } } } ajFileClose(&outf); ajSeqallDel(&seqall); ajSeqDel(&seq); ajStrDel(&seqid); embExit(); return 0; }