コード例 #1
0
ファイル: web.c プロジェクト: elmargb/kentUtils
void webPushErrHandlers(void)
/* Push warn and abort handler for errAbort(). */
{
if (webInTextMode)
    pushWarnHandler(textVaWarn);
else
    pushWarnHandler(webVaWarn);
pushAbortHandler(softAbort);
hDumpStackPushAbortHandler();
}
コード例 #2
0
boolean errCatchPushHandlers(struct errCatch *errCatch)
/* Push error handlers.  Not usually called directly. */
{
pushAbortHandler(errCatchAbortHandler);
pushWarnHandler(errCatchWarnHandler);
struct errCatch **pErrCatchStack = getStack();
slAddHead(pErrCatchStack, errCatch);
return TRUE;
}
コード例 #3
0
ファイル: runErr.c プロジェクト: davidhoover/kent
void _pf_punt_init()
/* Initialize punt/catch system.  Mostly just redirects the
 * errAbort handler. */
{
punter.message = dyStringNew(0);
punter.source = dyStringNew(0);
pushWarnHandler(puntWarnHandler);
pushAbortHandler(puntAbortHandler);
}
コード例 #4
0
static void cartJsonPushErrHandlers()
/* Push warn and abort handlers for errAbort. */
{
if (dyWarn == NULL)
    dyWarn = dyStringNew(0);
else
    dyStringClear(dyWarn);
pushWarnHandler(cartJsonVaWarn);
pushAbortHandler(cartJsonAbort);
}
コード例 #5
0
ファイル: edwScriptSubmitStatus.c プロジェクト: bowhan/kent
int main(int argc, char *argv[])
/* Process command line. */
{
if (!cgiIsOnWeb())
   usage();
cgiSpoof(&argc, argv);
pushWarnHandler(badRequestWarn);
edwScriptSubmitStatus();
return 0;
}
コード例 #6
0
ファイル: refineAli.c プロジェクト: davidhoover/kent
int test(int argc, char *argv[])
{
int start, stop;

if (argc != 9 && argc != 10)
    usageErr();
inName = argv[0];
cdnaName = argv[1];
chromDir = argv[2];
goodLogName = argv[3];
badLogName = argv[4];
unusualName = argv[5];
errName = argv[6];
start = atoi(argv[7]);
stop = atoi(argv[8]);
if (start >= stop)
    usageErr();
if (argc == 10)
    c2gName = argv[9];

inFile = mustOpen(inName, "r");
goodLogFile = mustOpen(goodLogName, "w");
badLogFile = mustOpen(badLogName, "w");
unusualFile = mustOpen(unusualName, "w");
errFile = mustOpen(errName, "w");
pushWarnHandler(reportWarning);

dnaUtilOpen();

printf("Loading chromosomes\n");
loadGenome(chromDir, &chroms, &chromNames, &chromCount);
startRedoHash();

printf("Analysing %s\n", inName);
if (weAreWeb())
    htmlHorizontalLine();

analyse(start, stop);

//endRedoHash();
freeGenome(&chroms, &chromNames, chromCount);
popWarnHandler();
fclose(inFile);
fclose(goodLogFile);
fclose(badLogFile);
fclose(unusualFile);
fclose(errFile);
return 0;
}
コード例 #7
0
ファイル: textOut.c プロジェクト: JinfengChen/pblat
struct pipeline *textOutInit(char *fileName, char *compressType)
/* Set up stdout to be HTTP text, file (if fileName is specified), or 
 * compressed file (if both fileName and compressType are specified -- 
 * see textOut.h for supported compression types).  
 * Return NULL if no compression, otherwise a pipeline handle on which 
 * textOutClose should be called when we're done writing stdout. */
{
struct pipeline *compressPipeline = NULL;

trimSpaces(fileName);
if (isEmpty(fileName))
    {
    printf("Content-Type: text/plain\n\n");
    }
else if (isEmpty(compressType) || sameWord(compressType, textOutCompressNone))
    {
    printf("Content-Type: application/octet-stream\n");
    printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
    }
else
    {
    char *suffix = getCompressSuffix(compressType);

    printf("Content-Type: application/x-%s\n", compressType);
    if (endsWith(fileName, suffix))
	printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
    else
	printf("Content-Disposition: attachment; filename=%s%s\n\n",
	       fileName, suffix);

    /* Send the Content header uncompressed! */
    fflush(stdout);

    /* Make sure no environment variables interfere with compressor. */
    cleanEnvVars(compressType);

    /* Redirect stdout to compressor pipeline object. */
    compressPipeline = pipelineOpen1(getCompressor(compressType),
				     pipelineWrite, NULL, NULL);
    if (-1 == dup2(pipelineFd(compressPipeline), STDOUT_FILENO))
	errnoAbort("dup2(pipelineFd %d, stdout %d) failed in textOpen()",
		   pipelineFd(compressPipeline), STDOUT_FILENO);
    }
pushWarnHandler(textOutWarnHandler);
pushAbortHandler(textOutAbortHandler);
return(compressPipeline);
}
コード例 #8
0
ファイル: edwWebSubmit.c プロジェクト: bowhan/kent
void doMiddle()
/* doMiddle - put up middle part of web page, not including http and html headers/footers */
{
pushWarnHandler(localWarn);
printf("<FORM ACTION=\"../cgi-bin/edwWebSubmit\" METHOD=GET>\n");
struct sqlConnection *conn = edwConnectReadWrite(edwDatabase);
userEmail = edwGetEmailAndVerify();
if (userEmail == NULL)
    logIn();
else if (cgiVarExists(stopButtonName))
    stopUpload(conn);
else if (cgiVarExists("submitUrl"))
    submitUrl(conn);
else if (cgiVarExists("monitor"))
    monitorSubmission(conn);
else
    getUrl(conn);
printf("</FORM>");
}
コード例 #9
0
int main(int argc, char *argv[])
{
char *sangerName, *jimName, *updateName, *errName;
struct g2cFile *sangerGenes, *jimGenes;
if (argc != 5)
    {
    errAbort("c2gcheck - compares two gene-to-cdna files, notes differences\n"
             "and writes out a third merged file.\n"
             "Usage:\n"
             "    c2gcheck Sanger Jim Update errs\n");
    }

memPool = lmInit(1<<16);
pushWarnHandler(reportWarning);

sangerName = argv[1];
jimName = argv[2];
updateName = argv[3];
errName = argv[4];

errFile = mustOpen(errName, "w");

sangerGenes = loadG2cFile(sangerName);
jimGenes = loadG2cFile(jimName);

checkOneFile(sangerGenes, sangerName);
checkOneFile(jimGenes, jimName);

checkTwoFiles(sangerGenes, jimGenes, "Jim unique");
checkTwoFiles(jimGenes, sangerGenes, "Sanger unique");

update(sangerGenes, jimGenes);

saveG2cFile(sangerGenes, updateName);

lmCleanup(&memPool);
return 0;
}
コード例 #10
0
ファイル: hgSuggest.c プロジェクト: ucscGenomeBrowser/kent
char *checkParams(char *database, char *prefix, char *type)
/* If we don't have valid CGI parameters, quit with a Bad Request HTTP response. */
{
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
    errAbort("%s", "Missing prefix and/or db CGI parameter");
if (! hDbIsActive(database))
    errAbort("'%s' is not a valid, active database", htmlEncode(database));
if (isNotEmpty(type) && differentString(type, ALT_OR_PATCH))
    errAbort("'%s' is not a valid type", type);
char *table = NULL;
if (! sameOk(type, ALT_OR_PATCH))
    {
    struct sqlConnection *conn = hAllocConn(database);
    table = connGeneSuggestTable(conn);
    hFreeConn(&conn);
    if(table == NULL)
        errAbort("gene autosuggest is not supported for db '%s'", database);
    }
popWarnHandler();
popAbortHandler();
return table;
}
コード例 #11
0
void fqToQa(char *inFile, char *outDir, char *outTabName)
/* fqToQa - convert from fq format with one big file to
 * format with one file per clone. */
{
struct lineFile *in;
FILE *out = NULL, *tab;
int lineSize;
char *line;
char ucscName[128];
char path[512];
static char lastPath[512];
int outFileCount = 0;
struct hash *uniqClone = newHash(16);
struct hash *uniqFrag = newHash(19);
boolean ignore = FALSE;

makeDir(outDir);
errLog = mustOpen("fqToQa.err", "w");
pushWarnHandler(warnHandler);
tab = mustOpen(outTabName, "w");
printf("Converting %s", inFile);
fflush(stdout);
in = lineFileOpen(inFile, TRUE);
while (lineFileNext(in, &line, &lineSize))
    {
    if (line[0] == '>')
	{
	ignore = FALSE;
	gsToUcsc(line+1, ucscName);
	faRecNameToQaFileName(outDir, ucscName, path);
	if (hashLookup(uniqFrag, ucscName))
	    {
	    ignore = TRUE;
	    warn("Duplicate %s in %s, ignoring all but first",
	    	ucscName, inFile);
	    }
	else
	    {
	    hashAdd(uniqFrag, ucscName, NULL);
	    }
	if (!sameString(path, lastPath))
	    {
	    strcpy(lastPath, path);
	    carefulClose(&out);
	    if (hashLookup(uniqClone, path))
		{
		warn("Duplicate %s in %s ignoring all but first", 
		    ucscName, inFile);
		}
	    else
		{
		hashAdd(uniqClone, path, NULL);
		out = mustOpen(path, "w");
		++outFileCount;
		if ((outFileCount&7) == 0)
		    {
		    putc('.', stdout);
		    fflush(stdout);
		    }
		}
	    }
	if (out != NULL && !ignore)
	    {
	    fprintf(out, ">%s\n", ucscName);
	    fprintf(tab, "%s\t%s\n", ucscName, line+1);
	    }
	}
    else
	{
	if (out != NULL && !ignore)
	    {
	    fputs(line, out);
	    fputc('\n', out);
	    }
	}
    }
carefulClose(&out);
fclose(tab);
lineFileClose(&in);
printf("Made %d .qa files in %s\n", outFileCount, outDir);
}
コード例 #12
0
ファイル: vcfClick.c プロジェクト: davidhoover/kent
static void vcfGenotypesDetails(struct vcfRecord *rec, struct trackDb *tdb, char **displayAls)
/* Print summary of allele and genotype frequency, plus collapsible section
 * with table of genotype details. */
{
struct vcfFile *vcff = rec->file;
if (vcff->genotypeCount == 0)
    return;
// Wrapper table for collapsible section:
puts("<TABLE>");
pushWarnHandler(ignoreEm);
vcfParseGenotypes(rec);
popWarnHandler();
// Tally genotypes and alleles for summary:
int refs = 0, alts = 0, unks = 0;
int refRefs = 0, refAlts = 0, altAlts = 0, gtUnk = 0, gtOther = 0, phasedGts = 0;
int i;
for (i = 0;  i < vcff->genotypeCount;  i++)
    {
    struct vcfGenotype *gt = &(rec->genotypes[i]);
    if (gt->isPhased)
	phasedGts++;
    if (gt->hapIxA == 0)
	refs++;
    else if (gt->hapIxA > 0)
	alts++;
    else
	unks++;
    if (!gt->isHaploid)
	{
	if (gt->hapIxB == 0)
	    refs++;
	else if (gt->hapIxB > 0)
	    alts++;
	else
	    unks++;
	if (gt->hapIxA == 0 && gt->hapIxB == 0)
	    refRefs++;
	else if (gt->hapIxA == 1 && gt->hapIxB == 1)
	    altAlts++;
	else if ((gt->hapIxA == 1 && gt->hapIxB == 0) ||
		 (gt->hapIxA == 0 && gt->hapIxB == 1))
	    refAlts++;
	else if (gt->hapIxA < 0 || gt->hapIxB < 0)
	    gtUnk++;
	else
	    gtOther++;
	}
    }
printf("<B>Genotype count:</B> %d", vcff->genotypeCount);
if (differentString(seqName, "chrY"))
    printf(" (%d phased)", phasedGts);
else
    printf(" (haploid)");
puts("<BR>");
int totalAlleles = refs + alts + unks;
double refAf = (double)refs/totalAlleles;
double altAf = (double)alts/totalAlleles;
printf("<B>Alleles:</B> %s: %d (%.3f%%); %s: %d (%.3f%%)",
       displayAls[0], refs, 100*refAf, displayAls[1], alts, 100*altAf);
if (unks > 0)
    printf("; unknown: %d (%.3f%%)", unks, 100 * (double)unks/totalAlleles);
puts("<BR>");
// Should be a better way to detect haploid chromosomes than comparison with "chrY":
if (vcff->genotypeCount > 1 && differentString(seqName, "chrY"))
    {
    printf("<B>Genotypes:</B> %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%)",
	   displayAls[0], displayAls[0], refRefs, 100*(double)refRefs/vcff->genotypeCount,
	   displayAls[0], displayAls[1], refAlts, 100*(double)refAlts/vcff->genotypeCount,
	   displayAls[1], displayAls[1], altAlts, 100*(double)altAlts/vcff->genotypeCount);
    if (gtUnk > 0)
	printf("; unknown: %d (%.3f%%)", gtUnk, 100*(double)gtUnk/vcff->genotypeCount);
    if (gtOther > 0)
	printf("; other: %d (%.3f%%)", gtOther, 100*(double)gtOther/vcff->genotypeCount);
    printf("<BR>\n");
    if (rec->alleleCount == 2)
	{
	boolean showHW = cartOrTdbBoolean(cart, tdb, VCF_SHOW_HW_VAR, FALSE);
	if (showHW)
	    printf("<B><A HREF=\"http://en.wikipedia.org/wiki/Hardy%%E2%%80%%93Weinberg_principle\" "
		   "TARGET=_BLANK>Hardy-Weinberg equilibrium</A>:</B> "
		   "P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%<BR>",
		   displayAls[0], displayAls[0], 100*refAf*refAf,
		   displayAls[0], displayAls[1], 100*2*refAf*altAf,
		   displayAls[1], displayAls[1], 100*altAf*altAf);
	}
    }
puts("<BR>");
vcfGenotypeTable(rec, tdb->track, displayAls);
puts("</TABLE>");
}
コード例 #13
0
ファイル: hgApi.c プロジェクト: davidhoover/kent
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
struct dyString *output = newDyString(10000);

setUdcCacheDir();
cgiSpoof(&argc, argv);
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);

char *database = cgiString("db");
char *cmd = cgiString("cmd");
char *jsonp = cgiOptionalString("jsonp");
if (!hDbExists(database))
    errAbort("Invalid database '%s'", database);

if (!strcmp(cmd, "defaultPos"))
    {
    dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database));
    }
else if (!strcmp(cmd, "metaDb"))
    {
    // Return list of values for given metaDb var
    // e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell

    struct sqlConnection *conn = hAllocConn(database);
    boolean metaDbExists = sqlTableExists(conn, "metaDb");
    if (metaDbExists)
        {
        char *var = cgiOptionalString("var");
        if (!var)
            errAbort("Missing var parameter");
        boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
        struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
                                                 !fileSearch, fileSearch);
        struct slPair *pair;
        dyStringPrintf(output, "[\n");
        for (pair = pairs; pair != NULL; pair = pair->next)
            {
            if (pair != pairs)
                dyStringPrintf(output, ",\n");
            dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)),
                           javaScriptLiteralEncode(mdbPairVal(pair)));
            }
        dyStringPrintf(output, "\n]\n");
        }
    else
        errAbort("Assembly does not support metaDb");
    }
// TODO: move to lib since hgTracks and hgApi share
#define METADATA_VALUE_PREFIX    "hgt_mdbVal"
else if (startsWith(METADATA_VALUE_PREFIX, cmd))
    {
    // Returns metaDb value control: drop down or free text, with or without help link.
    // e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell

    // TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share

    struct sqlConnection *conn = hAllocConn(database);
    boolean metaDbExists = sqlTableExists(conn, "metaDb");
    if (metaDbExists)
        {
        char *var = cgiOptionalString("var");
        if (!var)
            errAbort("Missing var parameter");

        int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
        if (ix == 0) //
            errAbort("Unsupported 'cmd' parameter");

        enum cvSearchable searchBy = cvSearchMethod(var);
        char name[128];
        safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
        if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
            {
            boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
            struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
                                                     !fileSearch, fileSearch);
            if (slCount(pairs) > 0)
                {
                char *dropDownHtml =
                                cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
                                                      name, pairs, NULL, ANYLABEL, "mdbVal",
                                                      "style='min-width: 200px; font-size: .9em;' "
                                                      "onchange='findTracksMdbValChanged(this);'");
                if (dropDownHtml)
                    {
                    dyStringAppend(output,dropDownHtml);
                    freeMem(dropDownHtml);
                    }
                slPairFreeList(&pairs);
                }
            }
        else if (searchBy == cvSearchByFreeText)
            {
            dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal freeText' "
                           "onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
                           "width:310px; font-size:.9em;'>", name);
            }
        else if (searchBy == cvSearchByWildList)
            {
            dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal wildList' "
                           "title='enter comma separated list of values' "
                           "onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
                           "width:310px; font-size:.9em;'>", name);
            }
        else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
            {
            // TO BE IMPLEMENTED
            }
        else
            errAbort("Metadata variable not searchable");

        dyStringPrintf(output,"<span id='helpLink%i'>&nbsp;</span>",ix);
        }
    else
        errAbort("Assembly does not support metaDb");
    }
else if (!strcmp(cmd, "tableMetadata"))
    { // returns an html table with metadata for a given track
    char *trackName = cgiOptionalString("track");
    boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel"));
    boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel"));
    if (trackName != NULL)
        {
        // hTrackDbForTrackAndAncestors avoids overhead of getting whole track list!
        struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName);
        if (tdb != NULL)
            {
            char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel);
            if (html)
                {
                dyStringAppend(output,html);
                freeMem(html);
                }
            else
                dyStringPrintf(output,"No metadata found for track %s.",trackName);
            }
        else
            dyStringPrintf(output,"Track %s not found",trackName);
        }
    else
        dyStringAppend(output,"No track variable found");
    }
else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos"))
    {
    char query[256];
    struct sqlResult *sr;
    char **row;
    struct genePred *gp;
    char *name = cgiString("name");
    char *table = cgiString("table");
    int num = cgiInt("num");
    struct sqlConnection *conn = hAllocConn(database);
    sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", table, name);
    sr = sqlGetResult(conn, query);
    if ((row = sqlNextRow(sr)) != NULL)
        {
        gp = genePredLoad(row);
        boolean found;
        int start, end;
        if (sameString(cmd, "codonToPos"))
            found = codonToPos(gp, num, &start, &end);
        else
            found = exonToPos(gp, num, &start, &end);
        if (found)
            dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end);
        else
            dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon");
        }
    else
        dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name);
    sqlFreeResult(&sr);
    hFreeConn(&conn);
    }
else
    {
    warn("unknown cmd: %s",cmd);
    errAbort("Unsupported 'cmd' parameter");
    }

apiOut(dyStringContents(output), jsonp);
cgiExitTime("hgApi", enteredMainTime);
return 0;
}
コード例 #14
0
ファイル: patSpace.c プロジェクト: davidhoover/kent
int main(int argc, char *argv[])
{
char *genoListName;
char *cdnaListName;
char *oocFileName;
char *pairFileName;
struct patSpace *patSpace;
long startTime, endTime;
char **genoList;
int genoListSize;
char *genoListBuf;
char **cdnaList;
int cdnaListSize;
char *cdnaListBuf;
char *genoName;
int i;
int estIx = 0;
struct dnaSeq **seqListList = NULL, *seq;
static char hitFileName[512], mergerFileName[512], okFileName[512];
char *outRoot;
struct hash *pairHash;

if (dumpMe)
    {
    bigHtmlFile = mustOpen("C:\\inetpub\\wwwroot\\test\\patAli.html", "w");
    littleHtmlFile = mustOpen("C:\\inetpub\\wwwroot\\test\\patSpace.html", "w");
    htmStart(bigHtmlFile, "PatSpace Alignments");
    htmStart(littleHtmlFile, "PatSpace Index");
    }

if ((hostName = getenv("HOST")) == NULL)
    hostName = "";

if (argc != 6)
    usage();

pushWarnHandler(patSpaceWarnHandler);
startTime = clock1000();
dnaUtilOpen();
makePolys();
genoListName = argv[1];
cdnaListName = argv[2];
oocFileName = argv[3];
pairFileName = argv[4];
outRoot = argv[5];

sprintf(hitFileName, "%s.hit", outRoot);
sprintf(mergerFileName, "%s.glu", outRoot);
sprintf(okFileName, "%s.ok", outRoot);

readAllWords(genoListName, &genoList, &genoListSize, &genoListBuf);
readAllWords(cdnaListName, &cdnaList, &cdnaListSize, &cdnaListBuf);
pairHash = makePairHash(pairFileName);

hitOut = mustOpen(hitFileName, "w");
mergerOut = mustOpen(mergerFileName, "w");
dumpOut = mustOpen("dump.out", "w");
seqListList = needMem(genoListSize*sizeof(seqListList[0]) );
fprintf(hitOut, "Pattern space 0.2 cDNA matcher\n");
fprintf(hitOut, "cDNA files: ", cdnaListSize);
for (i=0; i<cdnaListSize; ++i)
    fprintf(hitOut, " %s", cdnaList[i]);
fprintf(hitOut, "\n");
fprintf(hitOut, "%d genomic files\n", genoListSize);
for (i=0; i<genoListSize; ++i)
    {
    genoName = genoList[i];
    if (!startsWith("//", genoName)  )
        {
        seqListList[i] = seq = faReadAllDna(genoName);
        fprintf(hitOut, "%d els in %s ", slCount(seq), genoList[i]);
        for (; seq != NULL; seq = seq->next)
            fprintf(hitOut, "%d ", seq->size);
        fprintf(hitOut, "\n");
        }
    }

patSpace = makePatSpace(seqListList, genoListSize, oocFileName);

for (i=0; i<cdnaListSize; ++i)
    {
    FILE *f;
    char *estFileName;
    DNA *dna;
    char *estName;
    int size;
    int c;
    int maxSizeForFuzzyFind = 20000;
    int dotCount = 0;

    estFileName = cdnaList[i];
    if (startsWith("//", estFileName)  )
		continue;

    f = mustOpen(estFileName, "rb");
    while ((c = fgetc(f)) != EOF)
    if (c == '>')
        break;
    printf("%s", cdnaList[i]);
    fflush(stdout);
    while (fastFaReadNext(f, &dna, &size, &estName))
        {
	aliSeqName = estName;
        if (size < maxSizeForFuzzyFind)  /* Some day need to fix this somehow... */
            {
            struct hashEl *hel;
            struct cdnaAliList *calList = NULL;

            hel = hashLookup(pairHash, estName);
            if (hel != NULL)    /* Do pair processing. */
                {
                struct estPair *ep;
                struct seq *thisSeq, *otherSeq;

                ep = hel->val;
                if (hel->name == ep->name3)
                    {
                    thisSeq = &ep->seq3;
                    otherSeq = &ep->seq5;
                    }
                else
                    {
                    thisSeq = &ep->seq5;
                    otherSeq = &ep->seq3;
                    }
                if (otherSeq->dna == NULL)  /* First in pair - need to save sequence. */
                    {
                    thisSeq->size = size;
                    thisSeq->dna = needMem(size);
                    memcpy(thisSeq->dna, dna, size);
                    }
                else                        /* Second in pair - do gluing and free partner. */
                    {
                    char mergedName[64];
                    thisSeq->dna = dna;
                    thisSeq->size = size;
                    sprintf(mergedName, "%s_AND_%s", ep->name5, ep->name3);

                    patSpaceFindOne(patSpace, ep->seq5.dna, ep->seq5.size,
                        '+', '5', ep->name5, &calList);
                    reverseComplement(ep->seq5.dna, ep->seq5.size);
                    patSpaceFindOne(patSpace, ep->seq5.dna, ep->seq5.size,
                        '-', '5', ep->name5, &calList);
                    patSpaceFindOne(patSpace, ep->seq3.dna, ep->seq3.size,
                        '+', '3', ep->name3, &calList);
                    reverseComplement(ep->seq3.dna, ep->seq3.size);
                    patSpaceFindOne(patSpace, ep->seq3.dna, ep->seq3.size,
                        '-', '3', ep->name3, &calList);
                    slReverse(&calList);
                    writeMergers(calList, mergedName, genoList);

                    freez(&otherSeq->dna);
                    thisSeq->dna = NULL;
                    thisSeq->size =otherSeq->size = 0;
                    }
                }
            else
                {
                patSpaceFindOne(patSpace, dna, size, '+', '5', estName, &calList);
                reverseComplement(dna, size);
                patSpaceFindOne(patSpace, dna, size, '-', '5', estName, &calList);
                slReverse(&calList);
                writeMergers(calList, estName, genoList);
                }
            ++estIx;
            if ((estIx & 0xfff) == 0)
                {
                printf(".");
                ++dotCount;
                fflush(stdout);
                }
            }
        }
    printf("\n");
    }
aliSeqName = "";
printf("ffSubmitted %3d ffAccepted %3d ffOkScore %3d ffSolidMatch %2d\n",
    ffSubmitted, ffAccepted, ffOkScore, ffSolidMatch);

endTime = clock1000();

printf("Total time is %4.2f\n", 0.001*(endTime-startTime));

/* Write out file who's presense say's we succeeded */
    {
    FILE *f = mustOpen(okFileName, "w");
    fputs("ok", f);
    fclose(f);
    }

if (dumpMe)
    {
    htmEnd(bigHtmlFile);
    htmEnd(littleHtmlFile);
    }
return 0;
}
コード例 #15
0
ファイル: textOut.c プロジェクト: davidhoover/kent
struct pipeline *textOutInit(char *fileName, char *compressType, int *saveStdout)
/* Set up stdout to be HTTP text, file (if fileName is specified), or 
 * compressed file (if both fileName and compressType are specified -- 
 * see textOut.h for supported compression types).  
 * Return NULL if no compression, otherwise a pipeline handle on which 
 * textOutClose should be called when we're done writing stdout. */
{
struct pipeline *compressPipeline = NULL;

// if path contains a slash, we are outputting to a local file
boolean outToFile = (strchr(fileName, '/') != NULL);
if (outToFile)
    {
    FILE *f;
    f = fopen(fileName, "w");
    /* We want to capture stdout output to a file */
    fflush(stdout);
    int tempOut = dup(STDOUT_FILENO);
    if (saveStdout)
	*saveStdout = tempOut;
    dup2(fileno(f),STDOUT_FILENO);   /* closes STDOUT before setting it again */
    fclose(f);
    }

trimSpaces(fileName);
if (isEmpty(fileName))
    {
    printf("Content-Type: text/plain\n\n");
    }
else if (isEmpty(compressType) || sameWord(compressType, textOutCompressNone))
    {
    if (!outToFile)
	{
	printf("Content-Type: application/octet-stream\n");
	printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
	}
    }
else
    {

    if (!outToFile)
	{
	char *suffix = getCompressSuffix(compressType);
	printf("Content-Type: application/x-%s\n", compressType);
	if (endsWith(fileName, suffix))
	    printf("Content-Disposition: attachment; filename=%s\n\n", fileName);
	else
	    printf("Content-Disposition: attachment; filename=%s%s\n\n",
		   fileName, suffix);
	/* Send the Content header uncompressed! */
	fflush(stdout);
	}

    /* Make sure no environment variables interfere with compressor. */
    cleanEnvVars(compressType);

    /* Redirect stdout to compressor pipeline object. */
    compressPipeline = pipelineOpen1(getCompressor(compressType),
				     pipelineWrite, NULL, NULL);
    if (-1 == dup2(pipelineFd(compressPipeline), STDOUT_FILENO))
	errnoAbort("dup2(pipelineFd %d, stdout %d) failed in textOpen()",
		   pipelineFd(compressPipeline), STDOUT_FILENO);
    }
pushWarnHandler(textOutWarnHandler);
pushAbortHandler(textOutAbortHandler);
return(compressPipeline);
}
コード例 #16
0
ファイル: edwWebRegisterScript.c プロジェクト: bowhan/kent
void doMiddle()
/* Write what goes between BODY and /BODY */
{
pushWarnHandler(localWarn);
if (!cgiServerHttpsIsOn())
     usage();
struct sqlConnection *conn = edwConnectReadWrite();
printf("<FORM ACTION=\"edwWebRegisterScript\" METHOD=POST>\n");
printf("<B>Register Script with ENCODE Data Warehouse</B><BR>\n");
#ifdef SOON
uglyf("HTTP_AUTHENTICATION: '%s'<BR>\n", getenv("HTTP_AUTHENTICATION"));
uglyf("HTTP_AUTHORIZATION: '%s'<BR>\n", getenv("HTTP_AUTHORIZATION"));
dumpEnv(mainEnv);
#endif
if (userEmail == NULL)
    {
    printf("Please sign in:");
    printf("<INPUT TYPE=BUTTON NAME=\"signIn\" VALUE=\"sign in\" id=\"signin\">");
    }
else if (cgiVarExists("description"))
    {
    struct edwUser *user = edwUserFromEmail(conn, userEmail);
    if (user == NULL)
	edwWarnUnregisteredUser(userEmail);
    else
	{
	char password[HEXED_32_SIZE];
	edwRandomHexed32(password);
	char babyName[HEXED_32_SIZE];
	edwRandomBabble(babyName, sizeof(babyName));

	edwRegisterScript(conn, user, babyName, password, cgiString("description"));
	printf("Script now registered.<BR>\n");
	printf("The script user name is %s.<BR>\n", babyName);
	printf("The script password is %s.<BR>\n", password);
	printf("Please save the script user name and password somewhere. ");
	puts("Please pass these two and the URL");
	puts(" of your validated manifest file (validated.txt) to our server to submit data.");
	puts("Construct a URL of the form:<BR>");
	printf("<PRE>https://encodedcc.sdsc.edu/cgi-bin/edwScriptSubmit"
	       "?user=%s&password=%s&url=%s\n</PRE>", 
	       babyName, password,
	       cgiEncode("http://your.host.edu/your_dir/validated.txt"));
	puts("That is pass the CGI encoded variables user, password, and url to the ");
	puts("web services CGI at");
	puts("https://encodedcc.sdsc.edu/cgi-bin/edwScriptSubmit. ");
	puts("You can use the http://encodedcc.sdsc.edu/cgi-bin/edwWebBrowse site to ");
	puts("monitor your submission interactively. Please contact your wrangler if you ");
	puts("have any questions.<BR>");
	cgiMakeButton("submit", "Register another script");
	}
    printf(" ");
    edwPrintLogOutButton();
    }
else
    {
    struct edwUser *user = edwUserFromEmail(conn, userEmail);
    edwPrintLogOutButton();
    if (user == NULL)
	edwWarnUnregisteredUser(userEmail);
    else
	{
	printf("%s is authorized to register a new script<BR>\n", userEmail);
	printf("<BR>Script description:\n");
	cgiMakeTextVar("description", NULL, 80);
	cgiMakeSubmitButton();
	}
    }
printf("</FORM>\n");
}
コード例 #17
0
ファイル: vcfTrack.c プロジェクト: maximilianh/kent
static void vcfHapClusterDraw(struct track *tg, int seqStart, int seqEnd,
			      struct hvGfx *hvg, int xOff, int yOff, int width,
			      MgFont *font, Color color, enum trackVisibility vis)
/* Split samples' chromosomes (haplotypes), cluster them by center-weighted
 * alpha similarity, and draw in the order determined by clustering. */
{
struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
    return;
purple = hvGfxFindColorIx(hvg, 0x99, 0x00, 0xcc);
undefYellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
enum hapColorMode colorMode = getColorMode(tg->tdb);
pushWarnHandler(ignoreEm);
struct vcfRecord *rec;
for (rec = vcff->records;  rec != NULL;  rec = rec->next)
    vcfParseGenotypes(rec);
popWarnHandler();
unsigned short gtHapCount = 0;
int nRecords = slCount(vcff->records);
int centerIx = getCenterVariantIx(tg, seqStart, seqEnd, vcff->records);
// Limit the number of variants that we compare, to keep from timing out:
// (really what we should limit is the number of distinct haplo's passed to hacTree!)
// In the meantime, this should at least be a cart var...
int maxVariantsPerSide = 50;
int startIx = max(0, centerIx - maxVariantsPerSide);
int endIx = min(nRecords, centerIx+1 + maxVariantsPerSide);
struct hacTree *ht = NULL;
unsigned short *gtHapOrder = clusterHaps(vcff, centerIx, startIx, endIx, &gtHapCount, &ht);
struct vcfRecord *centerRec = NULL;
int ix;
// Unlike drawing order (last drawn is on top), the first mapBox gets priority,
// so map center variant before drawing & mapping other variants!
for (rec = vcff->records, ix=0;  rec != NULL;  rec = rec->next, ix++)
    {
    if (ix == centerIx)
	{
	centerRec = rec;
	mapBoxForCenterVariant(rec, hvg, tg, xOff, yOff, width);
	break;
	}
    }
for (rec = vcff->records, ix=0;  rec != NULL;  rec = rec->next, ix++)
    {
    boolean isClustered = (ix >= startIx && ix < endIx);
    if (ix != centerIx)
	drawOneRec(rec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, isClustered, FALSE,
		   colorMode);
    }
// Draw the center rec on top, outlined with black lines, to make sure it is very visible:
drawOneRec(centerRec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, TRUE, TRUE,
	   colorMode);
// Draw as much of the tree as can fit in the left label area:
int extraPixel = (colorMode == altOnlyMode) ? 1 : 0;
int hapHeight = tg->height- CLIP_PAD - 2*extraPixel;
struct yFromNodeHelper yHelper = {0, NULL, NULL};
initYFromNodeHelper(&yHelper, yOff+extraPixel, hapHeight, gtHapCount, gtHapOrder,
		    vcff->genotypeCount);
struct titleHelper titleHelper = { NULL, 0, 0, 0, 0, NULL, NULL };
initTitleHelper(&titleHelper, tg->track, startIx, centerIx, endIx, nRecords, vcff);
char *treeAngle = cartOrTdbString(cart, tg->tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
boolean drawRectangle = sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE);
drawTreeInLabelArea(ht, hvg, yOff+extraPixel, hapHeight+CLIP_PAD, &yHelper, &titleHelper,
		    drawRectangle);
}
コード例 #18
0
ファイル: edwWebDeprecate.c プロジェクト: bowhan/kent
void tryToDeprecate(struct sqlConnection *conn)
/* CGI variables are set - if possible deprecate, otherwise put up error message. */
{
pushWarnHandler(localWarn);
fileList = cgiString("fileList");
reason = cloneString(trimSpaces(cgiString("reason")));
if (isEmpty(reason))
   {
   warn("Please enter a reason for deprecation.");
   getFileListAndReason(conn);
   }
else
   {
   /* Go through list of accessions and make sure they are all well formed and correspond to files that exist. */
   boolean ok = TRUE;
   struct slName *accList = slNameListOfUniqueWords(cloneString(fileList), FALSE);
   struct slName *acc;
   struct slInt *idList = NULL, *idEl;
   for (acc = accList; acc != NULL; acc = acc->next)
       {
       char *licensePlate = acc->name;
       if (!startsWith(edwLicensePlatePrefix, licensePlate))
           {
	   ok = FALSE;
	   warn("%s is not an accession, doesn't start with %s", licensePlate, edwLicensePlatePrefix);
	   break;
	   }
	char query[256];
	sqlSafef(query, sizeof(query), "select fileId from edwValidFile where licensePlate='%s'", licensePlate);
	int id = sqlQuickNum(conn, query);
	if (id == 0)
	   {
	   ok = FALSE;
	   warn("%s - no such accession. ", licensePlate);
	   break;
	   }
	/* check to see is it ok tor deprecate this file */
	if (!okToDeprecateThisFile(conn, id, userEmail))
	    {
	    ok = FALSE;
	    warn("You can not deprecate %s which was originally uploaded by %s.\n",
	    licensePlate, edwFindOwnerNameFromFileId(conn, id));
	    warn("Please click the check box below to override this rule.");
	    break;
	    }

	idEl = slIntNew(id);
	slAddTail(&idList, idEl);
	}

    if (accList == NULL)
        {
	warn("Please enter some file accessions");
	ok = FALSE;
	}

    /* If a problem then put up page to try again,   otherwise do deprecation. */
    if (!ok)
        getFileListAndReason(conn);
    else
        {
	deprecateFileList(conn, idList, reason);
	printf("Deprecated %d files<BR>\n", slCount(idList));
	cgiMakeButton("submit", "Deprecate More Files");
	printf(" ");
	edwPrintLogOutButton();
	}
    }
}
コード例 #19
0
ファイル: errabort.c プロジェクト: JimKent/linearSat
void pushWarnAbort()
/* Push handler that will abort on warnings. */
{
pushWarnHandler(warnAbortHandler);
}
コード例 #20
0
ファイル: errabort.c プロジェクト: JimKent/linearSat
void pushSilentWarnHandler()
/* Set warning handler to be quiet.  Do a popWarnHandler to restore. */
{
pushWarnHandler(silentVaWarn);
}
コード例 #21
0
int main(int argc, char *argv[])
{
char *genoListName;
char *otherListName;
char *oocFileName;
char *typeName;
char *outName;
struct patSpace *patSpace;
long startTime, endTime;
char **genoList;
int genoListSize;
char *genoListBuf;
char **otherList;
int otherListSize;
char *otherListBuf;
char *genoName;
int i;
int blockCount = 0;
struct dnaSeq **seqListList = NULL, *seq = NULL;
char *outRoot;
struct sqlConnection *conn;
enum ffStringency stringency = ffCdna;
int seedSize = 10;
FILE *out;
boolean noHead = FALSE;
struct repeatTracker *rt;
struct hash *repeatHash = newHash(10);

hostName = getenv("HOST");
pushWarnHandler(warnHandler);

startTime = clock1();
cgiSpoof(&argc, argv);
minMatch = cgiOptionalInt("minMatch", minMatch);
maxBad = cgiOptionalInt("maxBad", maxBad);
minBases = cgiOptionalInt("minBases", minBases);

dnaUtilOpen();

#ifdef DEBUG
/* Hard wire command line input so don't have to type it in each 
 * time run the stupid Gnu debugger. */

genoListName = "pFoo/geno.lst";
otherListName = "pFoo/bacend.lst";
typeName = "genomic";
oocFileName = "/d/biodata/human/10.ooc";
outName = "pFoo/pFoo.psl";

#else

if (argc != 6 && argc != 7)
    usage();

genoListName = argv[1];
otherListName = argv[2];
typeName = argv[3];
oocFileName = argv[4];
if (sameWord(oocFileName, "none"))
    oocFileName = NULL;
outName = argv[5];
if (argc == 7)
    {
    if (sameWord("noHead", argv[6]))
	noHead = TRUE;
    else
	usage();
    }

#endif 

if (sameWord(typeName, "mRNA") || sameWord(typeName, "cDNA"))
    {
    stringency = ffCdna;
    }
else if (sameWord(typeName, "genomic"))
    {
    stringency = ffTight;
    }
else if (sameWord(typeName, "g2g"))
    {
    stringency = ffTight;
    veryTight = TRUE;
    seedSize = 11;
    }
else if (sameString(typeName, "asm"))
    {
    stringency = ffTight;
    avoidSelfSelf = TRUE;
    }
else
    {
    warn("Unrecognized otherType %s\n", typeName);
    usage();
    }

readAllWordsOrFa(genoListName, &genoList, &genoListSize, &genoListBuf);
filterMissingFiles(genoList, &genoListSize);
if (genoListSize <= 0)
    errAbort("There are no files that exist in %s\n", genoListName);
readAllWordsOrFa(otherListName, &otherList, &otherListSize, &otherListBuf);
if (otherListSize <= 0)
    errAbort("There are no files that exist in %s\n", otherListName);
filterMissingFiles(otherList, &otherListSize);
out = mustOpen(outName, "w");
if (!noHead)
    pslWriteHead(out);

AllocArray(seqListList, genoListSize);
for (i=0; i<genoListSize; ++i)
    {
    genoName = genoList[i];
    if (!startsWith("#", genoName)  )
        seqListList[i] = seq = faReadAllDna(genoName);
    for (;seq != NULL; seq = seq->next)
	{
	int size = seq->size;
	char *name = seq->name;
	struct hashEl *hel;
	AllocVar(rt);
	AllocArray(rt->repBytes, size);
	rt->seq = seq;
	if ((hel = hashLookup(repeatHash, name)) != NULL)
	    errAbort("Duplicate %s in %s\n", name, genoName);
	hashAdd(repeatHash, name, rt);
	}
    storeMasked(repeatHash, genoName);
    }

patSpace = makePatSpace(seqListList, genoListSize, seedSize, oocFileName, minMatch, 2000);
endTime = clock1();
printf("Made index in %ld seconds\n",  (endTime-startTime));
startTime = endTime;

for (i=0; i<otherListSize; ++i)
    {
    FILE *f;
    char *otherName;
    int c;
    int dotCount = 0;
    struct dnaSeq otherSeq;
    ZeroVar(&otherSeq);

    otherName = otherList[i];
    if (startsWith("#", otherName)  )
	continue;
    f = mustOpen(otherName, "r");
    while ((c = fgetc(f)) != EOF)
	if (c == '>')
	    break;
    printf("%s\n", otherName);
    fflush(stdout);
    while (faFastReadNext(f, &otherSeq.dna, &otherSeq.size, &otherSeq.name))
        {
	aliSeqName = otherSeq.name;
	oneStrand(patSpace, repeatHash, &otherSeq, FALSE, stringency, out);
	reverseComplement(otherSeq.dna, otherSeq.size);
	oneStrand(patSpace, repeatHash, &otherSeq, TRUE, stringency, out);
	aliSeqName = NULL;
        }
    fclose(f);
    }
freePatSpace(&patSpace);
endTime = clock1();
printf("Alignment time is %ld sec\n", (endTime-startTime));
startTime = endTime;
fclose(out);
return 0;
}
コード例 #22
0
void pushRHandlers() {
  pushAbortHandler(R_abortHandler);
  pushWarnHandler(R_warnHandler);  
}