lib/wormdna.c File Reference

#include "common.h"
#include "dnautil.h"
#include "dnaseq.h"
#include "fa.h"
#include "gdf.h"
#include "nt4.h"
#include "snof.h"
#include "wormdna.h"
#include "cda.h"
#include "sig.h"
#include "dystring.h"

Include dependency graph for wormdna.c:

Go to the source code of this file.

Functions
static void	getDirs ()
char *	wormFeaturesDir ()
char *	wormChromDir ()
char *	wormCdnaDir ()
char *	wormSangerDir ()
char *	wormGenieDir ()
char *	wormXenoDir ()
void	wormChromNames (char ***retNames, int *retNameCount)
int	wormChromIx (char *name)
char *	wormChromForIx (int ix)
char *	wormOfficialChromName (char *name)
static void	wormCdnaCache ()
void	wormCdnaUncache ()
void	wormFreeCdnaInfo (struct wormCdnaInfo *ci)
static char *	realInfoString (char *s)
static void	parseRestOfCdnaInfo (char *textInfo, struct wormCdnaInfo *retInfo)
void	wormFaCommentIntoInfo (char *faComment, struct wormCdnaInfo *retInfo)
boolean	wormCdnaInfo (char *name, struct wormCdnaInfo *retInfo)
boolean	wormCdnaSeq (char *name, struct dnaSeq **retDna, struct wormCdnaInfo *retInfo)
wormFeature *	newWormFeature (char *name, char *chrom, int start, int end, char typeByte)
static struct wormFeature *	scanChromOffsetFile (char *dir, char *suffix, bits32 signature, int nameOffset, char *chromId, int start, int end, int addEnd)
wormFeature *	wormCdnasInRange (char *chromId, int start, int end)
wormFeature *	wormSomeGenesInRange (char *chromId, int start, int end, char *gdfDir)
wormFeature *	wormGenesInRange (char *chromId, int start, int end)
wormFeature *	wormCosmidsInRange (char *chromId, int start, int end)
FILE *	wormOpenGoodAli ()
cdaAli *	wormCdaAlisInRange (char *chromId, int start, int end)
boolean	nextWormCdnaAndInfo (struct wormCdnaIterator *it, struct dnaSeq **retSeq, struct wormCdnaInfo *retInfo)
dnaSeq *	nextWormCdna (struct wormCdnaIterator *it)
boolean	wormSearchAllCdna (struct wormCdnaIterator **retSi)
void	freeWormCdnaIterator (struct wormCdnaIterator **pIt)
static boolean	isAllAlpha (char *s)
static boolean	isAllDigit (char *s)
boolean	wormIsOrfName (char *in)
boolean	wormIsGeneName (char *name)
slName *	wormGeneToOrfNames (char *name)
char *	wormGeneFirstOrfName (char *geneName)
boolean	wormGeneForOrf (char *orfName, char *geneNameBuf, int bufSize)
boolean	wormInfoForGene (char *orfName, struct wormCdnaInfo *retInfo)
boolean	getWormGeneDna (char *name, DNA **retDna, boolean upcExons)
boolean	getWormGeneExonDna (char *name, DNA **retDna)
static void	makeChromFileName (char *chromId, char *buf)
void	wormLoadNt4Genome (struct nt4Seq ***retNt4Seq, int *retNt4Count)
void	wormFreeNt4Genome (struct nt4Seq ***pNt4Seq)
int	wormChromSize (char *chrom)
DNA *	wormChromPart (char *chromId, int start, int size)
DNA *	wormChromPartExonsUpper (char *chromId, int start, int size)
void	wormClipRangeToChrom (char *chrom, int *pStart, int *pEnd)
boolean	wormParseChromRange (char *in, char **retChromId, int *retStart, int *retEnd)
boolean	wormIsChromRange (char *in)
boolean	wormFixupOrfName (char *name)
boolean	wormIsAltSplicedName (char *name)
static void	makeIsoformBaseName (char *name)
static boolean	findAltSpliceRange (char *name, struct snof *snof, FILE *f, char **retChrom, int *retStart, int *retEnd, char *retStrand)
boolean	wormGeneRange (char *name, char **retChrom, char *retStrand, int *retStart, int *retEnd)
boolean	wormIsNamelessCluster (char *name)
DNA *	wormGetNamelessClusterDna (char *name)
static void	wormCacheSomeGdf (struct wormGdfCache *cache)
void	wormUncacheSomeGdf (struct wormGdfCache *cache)
void	wormUncacheGdf ()
gdfGene *	wormGetSomeGdfGene (char *name, struct wormGdfCache *cache)
gdfGene *	wormGetGdfGene (char *name)
gdfGene *	wormGetSomeGdfGeneList (char *baseName, int baseNameSize, struct wormGdfCache *cache)
gdfGene *	wormGetGdfGeneList (char *baseName, int baseNameSize)
gdfGene *	wormGdfGenesInRange (char *chrom, int start, int end, struct wormGdfCache *geneFinder)
Variables
static char const	rcsid [] = "$Id: wormdna.c,v 1.10 2005/04/10 14:41:26 markd Exp $"
static char *	jkwebDir = NULL
static char *	cdnaDir = NULL
static char *	featDir = NULL
static char *	nt4Dir = NULL
static char *	sangerDir = NULL
static char *	genieDir = NULL
static char *	xenoDir = NULL
static char *	chromIds [] = {"i", "ii", "iii", "iv", "v", "x", "m", }
static struct snof *	cdnaSnof = NULL
static FILE *	cdnaFa = NULL
wormGdfCache	wormSangerGdfCache = {&sangerDir,NULL,NULL}
wormGdfCache	wormGenieGdfCache = {&genieDir,NULL,NULL}
wormGdfCache *	defaultGdfCache = &wormSangerGdfCache

---

Function Documentation

static boolean findAltSpliceRange	(	char *	name,
		struct snof *	snof,
		FILE *	f,
		char **	retChrom,
		int *	retStart,
		int *	retEnd,
		char *	retStrand
	)			[static]

Definition at line 940 of file wormdna.c.

References chopLine, wormFeature::end, FALSE, makeIsoformBaseName(), sameString, SEEK_SET, snofElementCount(), snofFindFirstStartingWith(), snofNameOffsetAtIx(), wormFeature::start, TRUE, and wormParseChromRange().

Referenced by wormGeneRange().

{
char baseName[64];
char bName[64];
int snIx, maxIx;
int start = 0x7fffffff;
int end = -start;
char lineBuf[128];
char *words[3];
int wordCount;
int baseNameSize;

strcpy(baseName, name);
makeIsoformBaseName(baseName);
baseNameSize = strlen(baseName);
if (!snofFindFirstStartingWith(snof, baseName, baseNameSize, &snIx))
    return FALSE;
maxIx = snofElementCount(snof);
for (;snIx < maxIx; ++snIx)
    {
    long offset;
    char *geneName;

    snofNameOffsetAtIx(snof, snIx, &geneName, &offset);
    if (strncmp(geneName, baseName, baseNameSize) != 0)
        break;
    strcpy(bName, geneName);
    makeIsoformBaseName(bName);
    if (sameString(baseName, bName))
        {
        int s, e;
        fseek(f, offset, SEEK_SET);
        fgets(lineBuf, sizeof(lineBuf), f);
        wordCount = chopLine(lineBuf, words);
        assert(wordCount == 3);
        wormParseChromRange(words[0], retChrom, &s, &e);
        *retStrand = words[1][0];
        if (start > s)
            start = s;
        if (end < e)
            end = e;
        }
    }
*retStart = start;
*retEnd = end;
return TRUE;
}

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void freeWormCdnaIterator

(

struct wormCdnaIterator **

pIt

)

Definition at line 478 of file wormdna.c.

References carefulClose(), wormCdnaIterator::faFile, and freez().

{
struct wormCdnaIterator *it = *pIt;
if (it != NULL)
    {
    carefulClose(&it->faFile);
    freez(pIt);
    }
}

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static void getDirs

(

)

[static]

Definition at line 31 of file wormdna.c.

References cdnaDir, cloneString(), featDir, firstWordInFile(), genieDir, jkwebDir, nt4Dir, sangerDir, and xenoDir.

Referenced by makeChromFileName(), wormCacheSomeGdf(), wormCdnaCache(), wormCdnaDir(), wormCdnasInRange(), wormChromDir(), wormCosmidsInRange(), wormFeaturesDir(), wormGeneRange(), wormGenesInRange(), wormGenieDir(), wormOpenGoodAli(), wormSangerDir(), wormSearchAllCdna(), and wormXenoDir().

{
if (jkwebDir == NULL)
    {
    char buf[512];
    
    /* Look up directory where directory pointer files are stored
     * in environment string if it's there. */
    if ((jkwebDir = getenv("JKWEB")) == NULL)
        jkwebDir = "";

    sprintf(buf, "%scdna.dir", jkwebDir);
    firstWordInFile(buf, buf, sizeof(buf));
    cdnaDir = cloneString(buf);

    sprintf(buf, "%sfeat.dir", jkwebDir);
    firstWordInFile(buf, buf, sizeof(buf));
    featDir = cloneString(buf);

    sprintf(buf, "%snt4.dir", jkwebDir);
    firstWordInFile(buf, buf, sizeof(buf));
    nt4Dir = cloneString(buf);

    sprintf(buf, "%ssanger/", featDir); 
    sangerDir = cloneString(buf);

    sprintf(buf, "%sgenie/", featDir);
    genieDir = cloneString(buf);

    sprintf(buf, "%sxeno.dir", jkwebDir);
    firstWordInFile(buf, buf, sizeof(buf));
    xenoDir = cloneString(buf);
    }
}

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boolean getWormGeneDna	(	char *	name,
		DNA **	retDna,
		boolean	upcExons
	)

Definition at line 656 of file wormdna.c.

References chromIds, gdfGene::chromIx, gdfGene::dataCount, gdfGene::dataPoints, FALSE, gdfFreeGene(), gdfGeneExtents(), gdfOffsetGene(), gdfRcGene(), slName::name, reverseComplement(), gdfGene::strand, toUpperN(), TRUE, wormChromPart(), wormGeneToOrfNames(), wormGenieGdfCache, wormGetSomeGdfGene(), wormIsGeneName(), and wormSangerGdfCache.

{
struct gdfGene *g;
struct slName *syn = NULL;
long lstart, lend;
int start, end;
int dnaSize;
DNA *dna;
struct wormGdfCache *gdfCache;

/* Translate biologist type name to cosmid.N name */
if (wormIsGeneName(name))
    {
    syn = wormGeneToOrfNames(name);
    if (syn != NULL)
        name = syn->name;
    }
if (strncmp(name, "g-", 2) == 0)
    gdfCache = &wormGenieGdfCache;
else
    gdfCache = &wormSangerGdfCache;
if ((g = wormGetSomeGdfGene(name, gdfCache)) == NULL)
    return FALSE;
gdfGeneExtents(g, &lstart, &lend);
start = lstart;
end = lend;
/* wormClipRangeToChrom(chromIds[g->chromIx], &start, &end); */
dnaSize = end-start;
*retDna = dna = wormChromPart(chromIds[g->chromIx], start, dnaSize);

gdfOffsetGene(g, -start);
if (g->strand == '-')
    {
    reverseComplement(dna, dnaSize);
    gdfRcGene(g, dnaSize);
    }
if (upcExons)
    {
    int i;
    struct gdfDataPoint *pt = g->dataPoints;
    for (i=0; i<g->dataCount; i += 2)
        {
        toUpperN(dna + pt[i].start, pt[i+1].start - pt[i].start);
        }
    }
gdfFreeGene(g);
return TRUE;
}

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boolean getWormGeneExonDna	(	char *	name,
		DNA **	retDna
	)

Definition at line 706 of file wormdna.c.

References chromIds, gdfGene::chromIx, cloneString(), gdfGene::dataCount, gdfGene::dataPoints, dyStringAppendN(), dyStringFree, FALSE, gdfFreeGene(), gdfGeneExtents(), gdfOffsetGene(), gdfRcGene(), slName::name, newDyString(), reverseComplement(), gdfGene::strand, dyString::string, TRUE, wormChromPart(), wormGeneToOrfNames(), wormGenieGdfCache, wormGetSomeGdfGene(), wormIsGeneName(), and wormSangerGdfCache.

{
struct gdfGene *g;
struct slName *syn = NULL;
long lstart, lend;
int start, end;
int dnaSize;
DNA *dna;
int i;
struct gdfDataPoint *pt = NULL;
struct wormGdfCache *gdfCache;
struct dyString *dy = newDyString(1000);
/* Translate biologist type name to cosmid.N name */
if (wormIsGeneName(name))
    {
    syn = wormGeneToOrfNames(name);
    if (syn != NULL)
        name = syn->name;
    }
if (strncmp(name, "g-", 2) == 0)
    gdfCache = &wormGenieGdfCache;
else
    gdfCache = &wormSangerGdfCache;
if ((g = wormGetSomeGdfGene(name, gdfCache)) == NULL)
    return FALSE;
gdfGeneExtents(g, &lstart, &lend);
start = lstart;
end = lend;
/*wormClipRangeToChrom(chromIds[g->chromIx], &start, &end);*/
dnaSize = end-start;
dna = wormChromPart(chromIds[g->chromIx], start, dnaSize);

gdfOffsetGene(g, -start);
if (g->strand == '-')
    {
    reverseComplement(dna, dnaSize);
    gdfRcGene(g, dnaSize);
    }
pt = g->dataPoints;
for (i=0; i<g->dataCount; i += 2)
    {
    dyStringAppendN(dy, (dna+pt[i].start), (pt[i+1].start - pt[i].start));
    }
*retDna = cloneString(dy->string);
dyStringFree(&dy);
gdfFreeGene(g);
return TRUE;
}

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static boolean isAllAlpha

(

char *

s

)

[static]

Definition at line 489 of file wormdna.c.

References FALSE, and TRUE.

Referenced by wormIsGeneName().

{
char c;
while ((c = *s++) != 0)
    {
    if (!isalpha(c)) return FALSE;
    }
return TRUE;
}

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static boolean isAllDigit

(

char *

s

)

[static]

Definition at line 500 of file wormdna.c.

References FALSE, and TRUE.

Referenced by wormIsGeneName().

{
char c;
while ((c = *s++) != 0)
    {
    if (!isdigit(c)) return FALSE;
    }
return TRUE;
}

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static void makeChromFileName	(	char *	chromId,
		char *	buf
	)			[static]

Definition at line 756 of file wormdna.c.

References getDirs(), and nt4Dir.

Referenced by wormChromPart(), wormChromSize(), and wormLoadNt4Genome().

{
getDirs();
sprintf(buf, "%s%s.nt4", nt4Dir, chromId);
}

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static void makeIsoformBaseName

(

char *

name

)

[static]

Definition at line 934 of file wormdna.c.

References wormIsAltSplicedName().

Referenced by findAltSpliceRange().

{
if (wormIsAltSplicedName(name))
    name[strlen(name)-1] = 0;
}

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struct wormFeature* newWormFeature	(	char *	name,
		char *	chrom,
		int	start,
		int	end,
		char	typeByte
	)			[read]

Definition at line 298 of file wormdna.c.

References wormFeature::chrom, wormFeature::end, wormFeature::name, name, needMem(), wormFeature::start, and wormFeature::typeByte.

Referenced by scanChromOffsetFile().

{
int size = sizeof(struct wormFeature) + strlen(name);
struct wormFeature *feat = needMem(size);
feat->chrom = chrom;
feat->start = start;
feat->end = end;
feat->typeByte = typeByte;
strcpy(feat->name, name);
return feat;
}

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struct dnaSeq* nextWormCdna

(

struct wormCdnaIterator *

it

)

[read]

Definition at line 458 of file wormdna.c.

References wormCdnaIterator::faFile, faReadOneDnaSeq(), and TRUE.

{
return faReadOneDnaSeq(it->faFile, "unknown", TRUE);
}

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boolean nextWormCdnaAndInfo	(	struct wormCdnaIterator *	it,
		struct dnaSeq **	retSeq,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 446 of file wormdna.c.

References wormCdnaIterator::faFile, FALSE, faReadNext(), TRUE, and wormFaCommentIntoInfo().

{
char *faComment;

if (!faReadNext(it->faFile, "unknown", TRUE, &faComment, retSeq))
    return FALSE;
wormFaCommentIntoInfo(faComment, retInfo);
return TRUE;
}

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static void parseRestOfCdnaInfo	(	char *	textInfo,
		struct wormCdnaInfo *	retInfo
	)			[static]

Definition at line 183 of file wormdna.c.

References ArraySize, wormCdnaInfo::cdsEnd, wormCdnaInfo::cdsStart, chopString(), wormCdnaInfo::description, errAbort(), FALSE, wormCdnaInfo::gene, wormCdnaInfo::isAdult, wormCdnaInfo::isEmbryonic, wormCdnaInfo::isHermaphrodite, wormCdnaInfo::isMale, wormCdnaInfo::knowEnd, wormCdnaInfo::knowStart, wormCdnaInfo::orientation, wormCdnaInfo::product, realInfoString(), sameString, and TRUE.

Referenced by wormFaCommentIntoInfo().

{
int wordCount;
char *words[32];
char *s;

wordCount = chopString(textInfo, "|", words, ArraySize(words));
if (wordCount < 8)
    errAbort("Expecting at least 8 fields in cDNA database, got %d", wordCount);
if ((s = realInfoString(words[0])) != NULL)
    retInfo->orientation = s[0];
retInfo->gene = realInfoString(words[1]);
retInfo->product = realInfoString(words[2]);
if ((s = realInfoString(words[3])) != NULL)
    {
    char *parts[2];
    int partCount;
    partCount = chopString(s, ".", parts, ArraySize(parts));
    if (partCount == 2)
        {
        retInfo->knowStart = retInfo->knowEnd = TRUE;
        if (parts[0][0] == '<')
            {
            retInfo->knowStart = FALSE;
            parts[0] += 1;
            }
        if (parts[1][0] == '>')
            {
            retInfo->knowEnd = FALSE;
            parts[1] += 1;
            }
        retInfo->cdsStart = atoi(parts[0]);
        retInfo->cdsEnd = atoi(parts[1]);
        }
    }
if ((s = realInfoString(words[4])) != NULL)
    {
    if (sameString("embryo", s))
        retInfo->isEmbryonic = TRUE;
    else if (sameString("adult", s))
        retInfo->isAdult = TRUE;
    }
if ((s = realInfoString(words[5])) != NULL)
    {
    if (sameString("herm", s))
        retInfo->isHermaphrodite = TRUE;
    else if (sameString("male", s))
        retInfo->isMale = TRUE;
    }

if ((s = realInfoString(words[6])) != NULL)
    {
    /* Reserved. Unused currently */
    }
retInfo->description = realInfoString(words[7]);
}

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static char* realInfoString

(

char *

s

)

[static]

Definition at line 176 of file wormdna.c.

Referenced by parseRestOfCdnaInfo().

{
if (s[0] == '?' && s[1] == 0) return NULL;
return s;
}

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static struct wormFeature* scanChromOffsetFile	(	char *	dir,
		char *	suffix,
		bits32	signature,
		int	nameOffset,
		char *	chromId,
		int	start,
		int	end,
		int	addEnd
	)			[static, read]

Definition at line 312 of file wormdna.c.

References bits32, errAbort(), freeMem(), mustOpen(), mustRead(), mustReadOne, name, needMem(), newWormFeature(), slAddHead, slReverse(), and wormFeature::typeByte.

Referenced by wormCdnasInRange(), wormCosmidsInRange(), and wormSomeGenesInRange().

{
FILE *f;
char fileName[512];
bits32 sig, nameSize, entryCount;
int entrySize;
int *entry;
char *name;
bits32 i;
struct wormFeature *list = NULL, *el;
char *typePt;
char typeByte;

sprintf(fileName, "%s%s%s", dir, chromId, suffix);
f = mustOpen(fileName, "rb");
mustReadOne(f, sig);
if (sig != signature)
    errAbort("Bad signature on %s", fileName);
mustReadOne(f, entryCount);
mustReadOne(f, nameSize);
entrySize = nameSize + nameOffset;
entry = needMem(entrySize + 1);
name = (char *)entry;
name += nameOffset;
typePt = name-1;
for (i=0; i<entryCount; ++i)
    {
    mustRead(f, entry, entrySize);
    if (entry[0] > end)
        break;
    if (entry[1] < start)
        continue;
    typeByte = *typePt;
    el = newWormFeature(name, chromId, entry[0], entry[1]+addEnd, typeByte);
    slAddHead(&list, el);
    }
slReverse(&list);
fclose(f);
freeMem(entry);
return list;
}

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static void wormCacheSomeGdf

(

struct wormGdfCache *

cache

)

[static]

Definition at line 1086 of file wormdna.c.

References bits32, errAbort(), wormGdfCache::file, getDirs(), glSig, mustOpen(), mustReadOne, wormGdfCache::pDir, wormGdfCache::snof, and snofMustOpen().

Referenced by wormGetSomeGdfGene(), and wormGetSomeGdfGeneList().

{
if (cache->snof == NULL)
    {
    char fileName[512];
    char *dir;
    bits32 sig;
    getDirs();
    dir = *(cache->pDir);
    sprintf(fileName, "%sgenes", dir);
    cache->snof = snofMustOpen(fileName);
    sprintf(fileName, "%sgenes.gdf", dir);
    cache->file = mustOpen(fileName, "rb");
    mustReadOne(cache->file, sig);
    if (sig != glSig)
        errAbort("%s is not a good file", fileName);
    }
}

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struct cdaAli* wormCdaAlisInRange	(	char *	chromId,
		int	start,
		int	end
	)			[read]

Definition at line 405 of file wormdna.c.

References AllocVar, alxSig, bits32, cdaLoadOne(), cdnaDir, errAbort(), mustOpen(), mustReadOne, readOne, SEEK_SET, slAddHead, slReverse(), and wormOpenGoodAli().

{
struct cdaAli *list = NULL, *el;
char fileName[512];
FILE *ixFile, *aliFile;
bits32 sig;
int s, e;
long fpos;

aliFile = wormOpenGoodAli();

sprintf(fileName, "%s%s.alx", cdnaDir, chromId);
ixFile = mustOpen(fileName, "rb");
mustReadOne(ixFile, sig);
if (sig != alxSig)
    errAbort("Bad signature on %s", fileName);

for (;;)
    {
    if (!readOne(ixFile, s))
        break;
    mustReadOne(ixFile, e);
    mustReadOne(ixFile, fpos);
    if (e <= start)
        continue;
    if (s >= end)
        break;
    AllocVar(el);
    fseek(aliFile, fpos, SEEK_SET);
    el = cdaLoadOne(aliFile);
    if (el == NULL)
        errAbort("Truncated cdnaAli file");
    slAddHead(&list, el);
    }
slReverse(&list);
fclose(aliFile);
fclose(ixFile);
return list;
}

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static void wormCdnaCache

(

)

[static]

Definition at line 145 of file wormdna.c.

References cdnaDir, cdnaFa, cdnaSnof, getDirs(), mustOpen(), and snofMustOpen().

Referenced by wormCdnaInfo(), and wormCdnaSeq().

{
getDirs();
if (cdnaSnof == NULL)
    {
    char buf[512];

    sprintf(buf, "%s%s", cdnaDir, "allcdna");
    cdnaSnof = snofMustOpen(buf);
    sprintf(buf, "%s%s", cdnaDir, "allcdna.fa");
    cdnaFa = mustOpen(buf, "rb");
    }
}

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char* wormCdnaDir

(

)

Definition at line 81 of file wormdna.c.

References cdnaDir, and getDirs().

{
getDirs();
return cdnaDir;
}

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boolean wormCdnaInfo	(	char *	name,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 261 of file wormdna.c.

References cdnaFa, cdnaSnof, cloneString(), errAbort(), FALSE, SEEK_SET, snofFindOffset(), TRUE, wormCdnaCache(), and wormFaCommentIntoInfo().

{
char commentBuf[512];
char *comment;
long offset;

wormCdnaCache();
if (!snofFindOffset(cdnaSnof, name, &offset))
    return FALSE;
fseek(cdnaFa, offset, SEEK_SET);
fgets(commentBuf, sizeof(commentBuf), cdnaFa);
if (commentBuf[0] != '>')
    errAbort("Expecting line starting with > in cDNA fa file.\nGot %s", commentBuf);
comment = cloneString(commentBuf);
wormFaCommentIntoInfo(comment, retInfo);
return TRUE;
}

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boolean wormCdnaSeq	(	char *	name,
		struct dnaSeq **	retDna,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 280 of file wormdna.c.

References cdnaFa, cdnaSnof, FALSE, faReadNext(), SEEK_SET, snofFindOffset(), TRUE, wormCdnaCache(), and wormFaCommentIntoInfo().

{
long offset;
char *faComment;
char **pFaComment = (retInfo == NULL ? NULL : &faComment);

wormCdnaCache();
if (!snofFindOffset(cdnaSnof, name, &offset))
    return FALSE;
fseek(cdnaFa, offset, SEEK_SET);
if (!faReadNext(cdnaFa, name, TRUE, pFaComment, retDna))
    return FALSE;
wormFaCommentIntoInfo(faComment, retInfo);
return TRUE;
}

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struct wormFeature* wormCdnasInRange	(	char *	chromId,
		int	start,
		int	end
	)			[read]

Definition at line 358 of file wormdna.c.

References cdnaDir, cdoSig, getDirs(), and scanChromOffsetFile().

{
/* This routine looks through the .CDO files made by cdnaOff
 */
getDirs();
return scanChromOffsetFile(cdnaDir, ".cdo", cdoSig, 2*sizeof(int)+1, 
    chromId, start, end, 0);
}

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void wormCdnaUncache

(

)

Definition at line 160 of file wormdna.c.

References carefulClose(), cdnaDir, cdnaFa, cdnaSnof, freez(), and snofClose().

{
snofClose(&cdnaSnof);
carefulClose(&cdnaFa);
freez(&cdnaDir);
}

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char* wormChromDir

(

)

Definition at line 74 of file wormdna.c.

References getDirs(), and nt4Dir.

{
getDirs();
return nt4Dir;
}

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char* wormChromForIx

(

int

ix

)

Definition at line 124 of file wormdna.c.

References ArraySize, and chromIds.

{
assert(ix >= 0 && ix <= ArraySize(chromIds));
return chromIds[ix];
}

int wormChromIx

(

char *

name

)

Definition at line 118 of file wormdna.c.

References chromIds, and stringIx.

Referenced by wormChromSize(), and wormOfficialChromName().

{
return stringIx(name, chromIds);
}

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void wormChromNames	(	char ***	retNames,
		int *	retNameCount
	)

Definition at line 111 of file wormdna.c.

References ArraySize, and chromIds.

Referenced by xenAlignWorm().

{
*retNames = chromIds;
*retNameCount = ArraySize(chromIds);
}

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DNA* wormChromPart	(	char *	chromId,
		int	start,
		int	size
	)

Definition at line 813 of file wormdna.c.

References makeChromFileName(), and nt4LoadPart().

Referenced by getWormGeneDna(), getWormGeneExonDna(), wormChromPartExonsUpper(), wormGetNamelessClusterDna(), and xenAlignWorm().

{
char fileName[512];
makeChromFileName(chromId, fileName);
return nt4LoadPart(fileName, start, size);
}

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DNA* wormChromPartExonsUpper	(	char *	chromId,
		int	start,
		int	size
	)

Definition at line 821 of file wormdna.c.

References gdfFreeGene(), gdfUpcExons(), wormFeature::name, name, wormFeature::next, slFreeList(), wormFeature::start, wormChromPart(), wormGenesInRange(), wormGetGdfGene(), and wormIsNamelessCluster().

{
DNA *dna = wormChromPart(chromId, start, size);
struct wormFeature *geneFeat = wormGenesInRange(chromId, start, start+size);
struct wormFeature *feat;

for (feat = geneFeat; feat != NULL; feat = feat->next)
    {
    char *name = feat->name;
    if (!wormIsNamelessCluster(name))
        {
        struct gdfGene *gene = wormGetGdfGene(name);
        gdfUpcExons(gene, feat->start, dna, size, start);
        gdfFreeGene(gene);
        }
    }
slFreeList(&geneFeat);
return dna;
}

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int wormChromSize

(

char *

chrom

)

Definition at line 791 of file wormdna.c.

References ArraySize, chromIds, errAbort(), makeChromFileName(), nt4BaseCount(), and wormChromIx().

Referenced by wormClipRangeToChrom().

{
static int sizes[ArraySize(chromIds)];
int ix;
int size;

if ((ix = wormChromIx(chrom)) < 0)
    errAbort("%s isn't a chromosome", chrom);
size = sizes[ix];

/* If we don't know it already have to get it from file. */
if (size == 0)
    {
    char fileName[512];
    makeChromFileName(chromIds[ix], fileName);
    size = sizes[ix] = nt4BaseCount(fileName);
    }
return size;
}

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void wormClipRangeToChrom	(	char *	chrom,
		int *	pStart,
		int *	pEnd
	)

Definition at line 842 of file wormdna.c.

References wormChromSize().

Referenced by wormParseChromRange(), and xenAlignWorm().

{
int chromEnd = wormChromSize(chrom);
int temp;

/* Swap ends if reversed. */
if (*pStart > *pEnd)
    {
    temp = *pEnd;
    *pEnd = *pStart;
    *pStart = temp;
    }
/* Generally speaking try to slide the range covered by
 * start-end inside the chromosome rather than just
 * truncating an end. */
if (*pStart < 0)
    {
    *pEnd -= *pStart;
    *pStart = 0;
    }
if (*pEnd > chromEnd)
    {
    *pStart -= *pEnd - chromEnd;
    *pEnd = chromEnd;
    }
/* This handles case where the range is larger than the chromosome. */
if (*pStart < 0)
    *pStart = 0;
}

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struct wormFeature* wormCosmidsInRange	(	char *	chromId,
		int	start,
		int	end
	)			[read]

Definition at line 385 of file wormdna.c.

References featDir, getDirs(), pgoSig, and scanChromOffsetFile().

{
/* This routine looks through the .COO files made by makePgo
 */
getDirs();
return scanChromOffsetFile(featDir, ".coo", pgoSig, 2*sizeof(int)+1,
    chromId, start, end, 1);
}

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void wormFaCommentIntoInfo	(	char *	faComment,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 241 of file wormdna.c.

References errAbort(), parseRestOfCdnaInfo(), and zeroBytes().

Referenced by nextWormCdnaAndInfo(), wormCdnaInfo(), wormCdnaSeq(), and wormInfoForGene().

{
if (retInfo)
    {
    char *s;
    zeroBytes(retInfo, sizeof(*retInfo));
    /* Separate out first word and use it as name. */
    s = strchr(faComment, ' ');
    if (s == NULL)
        errAbort("Expecting lots of info, just got %s", faComment);
    *s++ = 0;
    retInfo->name = faComment+1;
    retInfo->motherString = faComment;

    parseRestOfCdnaInfo(s, retInfo);
    }
}

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char* wormFeaturesDir

(

)

Definition at line 67 of file wormdna.c.

References featDir, and getDirs().

Referenced by wormGeneForOrf(), wormGeneToOrfNames(), and wormInfoForGene().

{
getDirs();
return featDir;
}

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boolean wormFixupOrfName

(

char *

name

)

Definition at line 909 of file wormdna.c.

References FALSE, tolowers(), toUpperN(), and TRUE.

Referenced by wormGeneRange().

{
char *dot = strrchr(name, '.');
if (dot == NULL)
    return FALSE;
toUpperN(name, dot-name);   /* First part always upper case. */
if (!isdigit(dot[1]))          /* Nameless cluster - just leave following digits be. */
    return TRUE;
else
    tolowers(dot+1);        /* Suffix is lower case. */
return TRUE;
}

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void wormFreeCdnaInfo

(

struct wormCdnaInfo *

ci

)

Definition at line 168 of file wormdna.c.

References freeMem(), wormCdnaInfo::motherString, and zeroBytes().

{
freeMem(ci->motherString);
zeroBytes(ci, sizeof(*ci));
}

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void wormFreeNt4Genome

(

struct nt4Seq ***

pNt4Seq

)

Definition at line 779 of file wormdna.c.

References ArraySize, chromIds, freeNt4(), and freez().

Referenced by xenAlignWorm().

{
struct nt4Seq **seqs;
int i;
if ((seqs = *pNt4Seq) == NULL)
    return;
for (i=0; i<ArraySize(chromIds); ++i)
    freeNt4(&seqs[i]);
freez(pNt4Seq);
}

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struct gdfGene* wormGdfGenesInRange	(	char *	chrom,
		int	start,
		int	end,
		struct wormGdfCache *	geneFinder
	)			[read]

Definition at line 1183 of file wormdna.c.

References errAbort(), name, slAddHead, slFreeList(), slReverse(), wormGenieDir(), wormGenieGdfCache, wormGetSomeGdfGene(), wormIsNamelessCluster(), wormSangerDir(), wormSangerGdfCache, and wormSomeGenesInRange().

{
char *dir = NULL;
struct gdfGene *gdfList = NULL, *gdf;
struct wormFeature *nameList, *name;

if (geneFinder == &wormSangerGdfCache)
    dir = wormSangerDir();
else if (geneFinder == &wormGenieGdfCache)
    dir = wormGenieDir();
else
    errAbort("Unknown geneFinder line %d of %s", __LINE__, __FILE__);

nameList = wormSomeGenesInRange(chrom, start, end, dir);
for (name = nameList; name != NULL; name = name->next)
    {
    char *n = name->name;
    if (!wormIsNamelessCluster(n))
        {
        gdf = wormGetSomeGdfGene(n, geneFinder);
        slAddHead(&gdfList, gdf);
        }
    }
slFreeList(&nameList);
slReverse(&gdfList);
return gdfList;
}

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char* wormGeneFirstOrfName

(

char *

geneName

)

Definition at line 578 of file wormdna.c.

References cloneString(), slName::name, name, slFreeList(), and wormGeneToOrfNames().

Referenced by wormInfoForGene().

{
struct slName *synList = wormGeneToOrfNames(geneName);
char *name;
if (synList == NULL)
    return NULL;
name = cloneString(synList->name);
slFreeList(&synList);
return name;
}

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boolean wormGeneForOrf	(	char *	orfName,
		char *	geneNameBuf,
		int	bufSize
	)

Definition at line 590 of file wormdna.c.

References chopLine, FALSE, mustOpen(), TRUE, and wormFeaturesDir().

{
FILE *f;
char fileName[512];
char lineBuf[512];
int nameLen = strlen(orfName);
boolean ok = FALSE;

sprintf(fileName, "%sorf2gene", wormFeaturesDir());
f = mustOpen(fileName, "r");
while (fgets(lineBuf, sizeof(lineBuf), f))
    {
    if (strncmp(lineBuf, orfName, nameLen) == 0 && lineBuf[nameLen] == ' ')
        {
        char *words[2];
        int wordCount;
        wordCount = chopLine(lineBuf, words);
        assert((int)strlen(words[1]) < bufSize);
        strncpy(geneNameBuf, words[1], bufSize);
        ok = TRUE;
        break;
        }
    }
fclose(f);
return ok;
}

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boolean wormGeneRange	(	char *	name,
		char **	retChrom,
		char *	retStrand,
		int *	retStart,
		int *	retEnd
	)

Definition at line 991 of file wormdna.c.

References chopLine, FALSE, featDir, findAltSpliceRange(), getDirs(), mustOpen(), slName::name, SEEK_SET, slFreeList(), snofFindOffset(), snofMustOpen(), touppers(), wormFixupOrfName(), wormGeneToOrfNames(), wormIsChromRange(), wormIsGeneName(), and wormParseChromRange().

Referenced by wormGetNamelessClusterDna().

{
static struct snof *c2gSnof = NULL, *c2cSnof = NULL;
static FILE *c2gFile = NULL, *c2cFile = NULL;
long offset;
char fileName[512];
struct slName *syn = NULL;
boolean ok;

if (wormIsChromRange(name))
    {
    *retStrand = '.';
    return wormParseChromRange(name, retChrom, retStart, retEnd);
    }

getDirs();

/* Translate biologist type name to cosmid.N name */
if (wormIsGeneName(name))
    {
    syn = wormGeneToOrfNames(name);
    if (syn != NULL)
        {
        name = syn->name;
        }
    }
if (wormFixupOrfName(name)) /* See if ORF, and if so make nice. */
    {
    if (c2gSnof == NULL)
        {
        sprintf(fileName, "%sc2g", featDir);
        c2gSnof = snofMustOpen(fileName);
        sprintf(fileName, "%sc2g", featDir);
        c2gFile = mustOpen(fileName, "rb");
        }
    ok = findAltSpliceRange(name, c2gSnof, c2gFile, retChrom, retStart, retEnd, retStrand);
    }
else    /* Lets say it's a cosmid. */
    {
    char lineBuf[128];
    char *words[3];
    int wordCount;
    touppers(name);
    if (c2cSnof == NULL)
        {
        sprintf(fileName, "%sc2c", featDir);
        c2cSnof = snofMustOpen(fileName);
        sprintf(fileName, "%sc2c", featDir);
        c2cFile = mustOpen(fileName, "rb");
        }
    if (!snofFindOffset(c2cSnof, name, &offset) )
        return FALSE;
    fseek(c2cFile, offset, SEEK_SET);
    fgets(lineBuf, sizeof(lineBuf), c2cFile);
    wordCount = chopLine(lineBuf, words);
    assert(wordCount == 3);
    assert(strcmp(words[2], name) == 0);
    assert(wormIsChromRange(words[0]));
    *retStrand = words[1][0];
    ok = wormParseChromRange(words[0], retChrom, retStart, retEnd);
    }
slFreeList(&syn);
return ok;
}

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struct wormFeature* wormGenesInRange	(	char *	chromId,
		int	start,
		int	end
	)			[read]

Definition at line 376 of file wormdna.c.

References getDirs(), sangerDir, and wormSomeGenesInRange().

Referenced by wormChromPartExonsUpper().

{
/* This routine looks through the .PGO files made by makePgo
 */
getDirs();
return wormSomeGenesInRange(chromId, start, end, sangerDir);
}

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struct slName* wormGeneToOrfNames

(

char *

name

)

[read]

Definition at line 539 of file wormdna.c.

References ArraySize, chopString(), errAbort(), errno, newSlName(), slAddTail(), tolowers(), whiteSpaceChopper, and wormFeaturesDir().

Referenced by getWormGeneDna(), getWormGeneExonDna(), wormGeneFirstOrfName(), and wormGeneRange().

{
struct slName *synList = NULL;
char synFileName[512];
FILE *synFile;
char lineBuf[128];
int nameLen = strlen(name);

/* genes are supposed to be lower case. */
tolowers(name);

/* Open synonym file and loop through each line of it */
sprintf(synFileName, "%ssyn", wormFeaturesDir());
if ((synFile = fopen(synFileName, "r")) == NULL)
    errAbort("Can't find synonym file '%s'. (errno: %d)\n", synFileName, errno);
while (fgets(lineBuf, ArraySize(lineBuf), synFile))
    {
    /* If first part of line matches chop up line. */
    if (strncmp(name, lineBuf, nameLen) == 0)
        {
        char *syns[32];
        int count;
        count = chopString(lineBuf, whiteSpaceChopper, syns, ArraySize(syns));

        /* Looks like we got a synonym.  Add all the aliases. */
        if (strcmp(name, syns[0]) == 0)
            {
            int i;
            for (i=1; i<count; ++i)
                slAddTail(&synList, newSlName(syns[i]));
            break;
            }
        }
    }
fclose(synFile);
return synList;
}

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char* wormGenieDir

(

)

Definition at line 95 of file wormdna.c.

References genieDir, and getDirs().

Referenced by wormGdfGenesInRange().

{
getDirs();
return genieDir;
}

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struct gdfGene* wormGetGdfGene

(

char *

name

)

[read]

Definition at line 1139 of file wormdna.c.

References defaultGdfCache, and wormGetSomeGdfGene().

Referenced by wormChromPartExonsUpper().

{
return wormGetSomeGdfGene(name, defaultGdfCache);
}

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struct gdfGene* wormGetGdfGeneList	(	char *	baseName,
		int	baseNameSize
	)			[read]

Definition at line 1177 of file wormdna.c.

References defaultGdfCache, and wormGetSomeGdfGeneList().

{
return wormGetSomeGdfGeneList(baseName, baseNameSize, defaultGdfCache);
}

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DNA* wormGetNamelessClusterDna

(

char *

name

)

Definition at line 1070 of file wormdna.c.

References errAbort(), wormChromPart(), and wormGeneRange().

{
char *chrom;
int start, end;
char strand;
if (!wormGeneRange(name, &chrom, &strand, &start, &end))
    errAbort("Can't find %s in database", name);
return wormChromPart(chrom, start, end-start);
}

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struct gdfGene* wormGetSomeGdfGene	(	char *	name,
		struct wormGdfCache *	cache
	)			[read]

Definition at line 1127 of file wormdna.c.

References wormGdfCache::file, gdfReadOneGene(), SEEK_SET, wormGdfCache::snof, snofFindOffset(), and wormCacheSomeGdf().

Referenced by getWormGeneDna(), getWormGeneExonDna(), wormGdfGenesInRange(), and wormGetGdfGene().

{
long offset;

wormCacheSomeGdf(cache);
if (!snofFindOffset(cache->snof, name, &offset) )
    return NULL;
fseek(cache->file, offset, SEEK_SET);
return gdfReadOneGene(cache->file);
}

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struct gdfGene* wormGetSomeGdfGeneList	(	char *	baseName,
		int	baseNameSize,
		struct wormGdfCache *	cache
	)			[read]

Definition at line 1145 of file wormdna.c.

References wormGdfCache::file, gdfReadOneGene(), SEEK_SET, slAddTail(), slReverse(), wormGdfCache::snof, snofElementCount(), snofFindFirstStartingWith(), snofNameOffsetAtIx(), and wormCacheSomeGdf().

Referenced by wormGetGdfGeneList().

{
int snIx;
int maxIx;
struct snof *snof;
FILE *f;
struct gdfGene *list = NULL, *el;

wormCacheSomeGdf(cache);
snof = cache->snof;
f = cache->file;
if (!snofFindFirstStartingWith(snof, baseName, baseNameSize, &snIx))
    return NULL;

maxIx = snofElementCount(snof);
for (;snIx < maxIx; ++snIx)
    {
    long offset;
    char *geneName;

    snofNameOffsetAtIx(snof, snIx, &geneName, &offset);
    if (strncmp(geneName, baseName, baseNameSize) != 0)
        break;
    fseek(f, offset, SEEK_SET);
    el = gdfReadOneGene(f);
    slAddTail(&list, el);
    }
slReverse(&list);
return list;
}

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boolean wormInfoForGene	(	char *	orfName,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 618 of file wormdna.c.

References cloneString(), FALSE, freeMem(), mustOpen(), TRUE, wormFaCommentIntoInfo(), wormFeaturesDir(), wormGeneFirstOrfName(), and wormIsGeneName().

{
FILE *f;
char fileName[512];
char lineBuf[512];
int nameLen;
char *info = NULL;
char *synName = NULL;
int lineCount = 0;

/* Make this one work for orfs as well as gene names */
if (wormIsGeneName(orfName))
    {
    synName = wormGeneFirstOrfName(orfName);
    if (synName != NULL)
        orfName = synName;
    }
sprintf(fileName, "%sorfInfo", wormFeaturesDir());
nameLen = strlen(orfName);
f = mustOpen(fileName, "r");
while (fgets(lineBuf, sizeof(lineBuf), f))
    {
    ++lineCount;
    if (strncmp(lineBuf, orfName, nameLen) == 0 && lineBuf[nameLen] == ' ')
        {
        info = cloneString(lineBuf);
        break;
        }
    }
freeMem(synName);
fclose(f);
if (info == NULL)
    return FALSE;
wormFaCommentIntoInfo(info, retInfo);
return TRUE;;
}

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boolean wormIsAltSplicedName

(

char *

name

)

Definition at line 923 of file wormdna.c.

References FALSE.

Referenced by makeIsoformBaseName().

{
char *dot = strrchr(name, '.');
if (dot == NULL)
    return FALSE;
if (!isdigit(dot[1]))
    return FALSE;
return isalpha(dot[strlen(dot)-1]);
}

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boolean wormIsChromRange

(

char *

in

)

Definition at line 898 of file wormdna.c.

References wormFeature::end, wormFeature::start, and wormParseChromRange().

Referenced by wormGeneRange().

{
char *chromId;
int start, end;
boolean ok;
ok =  wormParseChromRange(in, &chromId, &start, &end);
return ok;
}

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boolean wormIsGeneName

(

char *

name

)

Definition at line 518 of file wormdna.c.

References chopString(), FALSE, isAllAlpha(), and isAllDigit().

Referenced by getWormGeneDna(), getWormGeneExonDna(), wormGeneRange(), and wormInfoForGene().

{
char buf[128];
int partCount;
strncpy(buf, name, sizeof(buf));
partCount = chopString(buf, "-", NULL, 0);
if (partCount == 2)
    {
    char *parts[2];
    chopString(buf, "-", parts, 2);
    return isAllAlpha(parts[0]) && isAllDigit(parts[1]);
    }
else
    {
    return FALSE;
    }
}

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boolean wormIsNamelessCluster

(

char *

name

)

Definition at line 1057 of file wormdna.c.

References FALSE, and TRUE.

Referenced by wormChromPartExonsUpper(), and wormGdfGenesInRange().

{
char *e = strrchr(name, '.');
if (e == NULL)
    return FALSE;
if (e[1] != 'N')
    return FALSE;
if (!isdigit(e[2]))
    return FALSE;
return TRUE;
}

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boolean wormIsOrfName

(

char *

in

)

Definition at line 511 of file wormdna.c.

{
return strchr(in, '.') != NULL;
}

void wormLoadNt4Genome	(	struct nt4Seq ***	retNt4Seq,
		int *	retNt4Count
	)

Definition at line 762 of file wormdna.c.

References ArraySize, chromIds, loadNt4(), makeChromFileName(), and needMem().

Referenced by xenAlignWorm().

{
int count = ArraySize(chromIds);
struct nt4Seq **nt4s = needMem(count*sizeof(*nt4s));
int i;
char fileName[512];

for (i=0; i<count; ++i)
    {
    makeChromFileName(chromIds[i], fileName);
    nt4s[i] = loadNt4(fileName, chromIds[i]);
    }
*retNt4Seq = nt4s;
*retNt4Count = count;
}

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char* wormOfficialChromName

(

char *

name

)

Definition at line 131 of file wormdna.c.

References chromIds, and wormChromIx().

Referenced by wormParseChromRange().

{
int ix = wormChromIx(name);
if (ix < 0) return NULL;
return chromIds[ix];
}

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FILE* wormOpenGoodAli

(

)

Definition at line 395 of file wormdna.c.

References cdaOpenVerify(), cdnaDir, and getDirs().

Referenced by wormCdaAlisInRange().

{
char fileName[512];
getDirs();
sprintf(fileName, "%sgood.ali", cdnaDir);
return cdaOpenVerify(fileName);
}

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boolean wormParseChromRange	(	char *	in,
		char **	retChromId,
		int *	retStart,
		int *	retEnd
	)

Definition at line 873 of file wormdna.c.

References ArraySize, chopString(), FALSE, TRUE, wormClipRangeToChrom(), and wormOfficialChromName().

Referenced by findAltSpliceRange(), wormGeneRange(), and wormIsChromRange().

{
char *words[5];
int wordCount;
char *chromId;
char buf[128];

strncpy(buf, in, sizeof(buf));
wordCount = chopString(buf, "- \t\r\n:", words, ArraySize(words));
if (wordCount != 3)
    return FALSE;
chromId = wormOfficialChromName(words[0]);
if (chromId == NULL)
    return FALSE;
if (!isdigit(words[1][0]) || !isdigit(words[2][0]))
    return FALSE;
*retChromId = chromId;
*retStart = atoi(words[1]);
*retEnd = atoi(words[2]);
wormClipRangeToChrom(chromId, retStart, retEnd);
return TRUE;
}

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char* wormSangerDir

(

)

Definition at line 88 of file wormdna.c.

References getDirs(), and sangerDir.

Referenced by wormGdfGenesInRange().

{
getDirs();
return sangerDir;
}

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boolean wormSearchAllCdna

(

struct wormCdnaIterator **

retSi

)

Definition at line 464 of file wormdna.c.

References cdnaDir, getDirs(), mustOpen(), needMem(), and TRUE.

{
char buf[512];
struct wormCdnaIterator *it;

it = needMem(sizeof(*it));
getDirs();
sprintf(buf, "%s%s", cdnaDir, "allcdna.fa");
it->faFile = mustOpen(buf, "rb");
*retSi = it;
return TRUE;
}

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struct wormFeature* wormSomeGenesInRange	(	char *	chromId,
		int	start,
		int	end,
		char *	gdfDir
	)			[read]

Definition at line 369 of file wormdna.c.

References pgoSig, and scanChromOffsetFile().

Referenced by wormGdfGenesInRange(), and wormGenesInRange().

{
return scanChromOffsetFile(gdfDir, ".pgo", pgoSig, 2*sizeof(int)+1,
    chromId, start, end, 0);
}

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void wormUncacheGdf

(

)

Definition at line 1121 of file wormdna.c.

References defaultGdfCache, and wormUncacheSomeGdf().

{
wormUncacheSomeGdf(defaultGdfCache);
}

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void wormUncacheSomeGdf

(

struct wormGdfCache *

cache

)

Definition at line 1114 of file wormdna.c.

References carefulClose(), wormGdfCache::file, wormGdfCache::snof, and snofClose().

Referenced by wormUncacheGdf().

{
snofClose(&cache->snof);
carefulClose(&cache->file);
}

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char* wormXenoDir

(

)

Definition at line 102 of file wormdna.c.

References getDirs(), and xenoDir.

{
getDirs();
return xenoDir;
}

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Variable Documentation

char* cdnaDir = NULL [static]

Definition at line 24 of file wormdna.c.

Referenced by getDirs(), wormCdaAlisInRange(), wormCdnaCache(), wormCdnaDir(), wormCdnasInRange(), wormCdnaUncache(), wormOpenGoodAli(), and wormSearchAllCdna().

FILE* cdnaFa = NULL [static]

Definition at line 143 of file wormdna.c.

Referenced by flyCdnaSeq(), wormCdnaCache(), wormCdnaInfo(), wormCdnaSeq(), and wormCdnaUncache().

struct snof* cdnaSnof = NULL [static]

Definition at line 142 of file wormdna.c.

Referenced by flyCdnaSeq(), wormCdnaCache(), wormCdnaInfo(), wormCdnaSeq(), and wormCdnaUncache().

char* chromIds[] = {"i", "ii", "iii", "iv", "v", "x", "m", } [static]

Definition at line 109 of file wormdna.c.

Referenced by getWormGeneDna(), getWormGeneExonDna(), wormChromForIx(), wormChromIx(), wormChromNames(), wormChromSize(), wormFreeNt4Genome(), wormLoadNt4Genome(), and wormOfficialChromName().

struct wormGdfCache* defaultGdfCache = &wormSangerGdfCache

Definition at line 1083 of file wormdna.c.

Referenced by wormGetGdfGene(), wormGetGdfGeneList(), and wormUncacheGdf().

char* featDir = NULL [static]

Definition at line 25 of file wormdna.c.

Referenced by getDirs(), wormCosmidsInRange(), wormFeaturesDir(), and wormGeneRange().

char* genieDir = NULL [static]

Definition at line 28 of file wormdna.c.

Referenced by getDirs(), and wormGenieDir().

char* jkwebDir = NULL [static]

Definition at line 22 of file wormdna.c.

Referenced by _cgiDir(), and getDirs().

char* nt4Dir = NULL [static]

Definition at line 26 of file wormdna.c.

Referenced by getDirs(), makeChromFileName(), and wormChromDir().

char const rcsid[] = "$Id: wormdna.c,v 1.10 2005/04/10 14:41:26 markd Exp $" [static]

Definition at line 20 of file wormdna.c.

char* sangerDir = NULL [static]

Definition at line 27 of file wormdna.c.

Referenced by getDirs(), wormGenesInRange(), and wormSangerDir().

struct wormGdfCache wormGenieGdfCache = {&genieDir,NULL,NULL}

Definition at line 1082 of file wormdna.c.

Referenced by getWormGeneDna(), getWormGeneExonDna(), and wormGdfGenesInRange().

struct wormGdfCache wormSangerGdfCache = {&sangerDir,NULL,NULL}

Definition at line 1081 of file wormdna.c.

Referenced by getWormGeneDna(), getWormGeneExonDna(), and wormGdfGenesInRange().

char* xenoDir = NULL [static]

Definition at line 29 of file wormdna.c.

Referenced by getDirs(), and wormXenoDir().

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