lib/blastOut.c File Reference

#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "axt.h"
#include "obscure.h"
#include "genoFind.h"

Include dependency graph for blastOut.c:

Go to the source code of this file.

Data Structures
struct	axtRef
struct	targetHits
Functions
static int	axtRefCmpScore (const void *va, const void *vb)
static void	targetHitsFree (struct targetHits **pObj)
static void	targetHitsFreeList (struct targetHits **pList)
static int	targetHitsCmpScore (const void *va, const void *vb)
static int	blastzToWublastScore (int bzScore)
static double	blastzScoreToWuBits (int bzScore, boolean isProt)
static double	blastzScoreToWuExpectation (int bzScore, double databaseSize)
static int	blastzScoreToNcbiBits (int bzScore)
static int	blastzScoreToNcbiScore (int bzScore)
static double	blastzScoreToNcbiExpectation (int bzScore)
static double	expectationToProbability (double e)
static int	countMatches (char *a, char *b, int size)
static int	countGaps (char *a, char *b, int size)
static int	countGapOpens (char *a, char *b, int size)
static int	countPositives (char *a, char *b, int size)
static int	plusStrandPos (int pos, int size, char strand, boolean isEnd)
static int	calcDigitCount (struct axt *axt, int tSize, int qSize)
static void	blastiodAxtOutput (FILE *f, struct axt *axt, int tSize, int qSize, int lineSize, boolean isProt, boolean isTranslated)
static struct targetHits *	bundleIntoTargets (struct axtBundle *abList)
static char *	nameForStrand (char strand)
static char *	progType (boolean isProt, struct axtBundle *ab, boolean isUpper)
static void	wuBlastOut (struct axtBundle *abList, int queryIx, boolean isProt, FILE *f, char *databaseName, int databaseSeqCount, double databaseLetterCount, char *ourId)
static void	ncbiPrintE (FILE *f, double e)
static void	ncbiBlastOut (struct axtBundle *abList, int queryIx, boolean isProt, FILE *f, char *databaseName, int databaseSeqCount, double databaseLetterCount, char *ourId, double minIdentity)
static void	xmlBlastOut (struct axtBundle *abList, int queryIx, boolean isProt, FILE *f, char *databaseName, int databaseSeqCount, double databaseLetterCount, char *ourId)
static void	printAxtTargetBlastTab (FILE *f, struct axt *axt, int targetSize)
static void	tabBlastOut (struct axtBundle *abList, int queryIx, boolean isProt, FILE *f, char *databaseName, int databaseSeqCount, double databaseLetterCount, char *ourId, boolean withComment)
void	axtBlastOut (struct axtBundle *abList, int queryIx, boolean isProt, FILE *f, char *databaseName, int databaseSeqCount, double databaseLetterCount, char *blastType, char *ourId, double minIdentity)
Variables
static char const	rcsid [] = "$Id: blastOut.c,v 1.26 2006/03/10 17:43:36 angie Exp $"
int	answer_for_kg

---

Function Documentation

void axtBlastOut	(	struct axtBundle *	abList,
		int	queryIx,
		boolean	isProt,
		FILE *	f,
		char *	databaseName,
		int	databaseSeqCount,
		double	databaseLetterCount,
		char *	blastType,
		char *	ourId,
		double	minIdentity
	)

Definition at line 782 of file blastOut.c.

References errAbort(), FALSE, ncbiBlastOut(), sameWord, tabBlastOut(), TRUE, wuBlastOut(), and xmlBlastOut().

Referenced by blastQueryOut().

                               :
 *   ab - the list of bundles of axt's. 
 *   f  - output file handle
 *   databaseSeqCount - number of sequences in database
 *   databaseLetterCount - number of bases or aa's in database
 *   blastType - blast/wublast/blast8/blast9/xml
 *   ourId - optional (may be NULL) thing to put in header
 */
{
if (abList == NULL)
    return;
if (sameWord(blastType, "wublast"))
    wuBlastOut(abList, queryIx, isProt, f, databaseName,
        databaseSeqCount, databaseLetterCount, ourId);
else if (sameWord(blastType, "xml"))
    xmlBlastOut(abList, queryIx, isProt, f, databaseName,
        databaseSeqCount, databaseLetterCount, ourId);
else if (sameWord(blastType, "blast"))
    ncbiBlastOut(abList, queryIx, isProt, f, databaseName,
        databaseSeqCount, databaseLetterCount, ourId, minIdentity);
else if (sameWord(blastType, "blast8"))
    tabBlastOut(abList, queryIx, isProt, f, databaseName,
        databaseSeqCount, databaseLetterCount, ourId, FALSE);
else if (sameWord(blastType, "blast9"))
    tabBlastOut(abList, queryIx, isProt, f, databaseName,
        databaseSeqCount, databaseLetterCount, ourId, TRUE);
else
    errAbort("Unrecognized blastType %s in axtBlastOut", blastType);
}

Here is the call graph for this function:

Here is the caller graph for this function:

static int axtRefCmpScore	(	const void *	va,
		const void *	vb
	)			[static]

Definition at line 18 of file blastOut.c.

References axtRef::axt, and axt::score.

{
const struct axtRef *a = *((struct axtRef **)va);
const struct axtRef *b = *((struct axtRef **)vb);
return b->axt->score - a->axt->score;
}

static void blastiodAxtOutput	(	FILE *	f,
		struct axt *	axt,
		int	tSize,
		int	qSize,
		int	lineSize,
		boolean	isProt,
		boolean	isTranslated
	)			[static]

Definition at line 228 of file blastOut.c.

References axtScoreSchemeProteinDefault(), calcDigitCount(), FALSE, plusStrandPos(), axt::qStart, axt::qStrand, axt::qSym, ss, axt::symCount, TRUE, axt::tStart, axt::tStrand, and axt::tSym.

Referenced by wuBlastOut().

{
int tOff = axt->tStart;
int dt = (isTranslated ? 3 : 1);
int qOff = axt->qStart;
int lineStart, lineEnd, i;
int digits = calcDigitCount(axt, tSize, qSize);
struct axtScoreScheme *ss = NULL;

if (isProt)
    ss = axtScoreSchemeProteinDefault();
for (lineStart = 0; lineStart < axt->symCount; lineStart = lineEnd)
    {
    lineEnd = lineStart + lineSize;
    if (lineEnd > axt->symCount) lineEnd = axt->symCount;
    fprintf(f, "Query: %-*d ", digits, plusStrandPos(qOff, qSize, axt->qStrand, FALSE));
    for (i=lineStart; i<lineEnd; ++i)
        {
        char c = axt->qSym[i];
        fputc(c, f);
        if (c != '-')
            ++qOff;
        }
    fprintf(f, " %-d\n", plusStrandPos(qOff, qSize, axt->qStrand, TRUE));
    fprintf(f, "       %*s ", digits, " ");
    for (i=lineStart; i<lineEnd; ++i)
        {
        char q, t, c;
        q = axt->qSym[i];
        t = axt->tSym[i];
        if (isProt)
            {
            if (q == t)
                c = q;
            else if (ss->matrix[(int)q][(int)t] > 0)
                c = '+';
            else
                c = ' ';
            }
        else
            c = ((toupper(q) == toupper(t)) ? '|' : ' ');

        fputc(c, f);
        }
    fprintf(f, "\n");
    fprintf(f, "Sbjct: %-*d ", digits, plusStrandPos(tOff, tSize, axt->tStrand, FALSE));
    for (i=lineStart; i<lineEnd; ++i)
        {
        char c = axt->tSym[i];
        fputc(c, f);
        if (c != '-')
            tOff += dt;
        }
    fprintf(f, " %-d\n", plusStrandPos(tOff, tSize, axt->tStrand, TRUE));
    fprintf(f, "\n");
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static int blastzScoreToNcbiBits

(

int

bzScore

)

[static]

Definition at line 101 of file blastOut.c.

References round.

Referenced by ncbiBlastOut(), tabBlastOut(), and xmlBlastOut().

{
return round(bzScore * 0.0205);
}

Here is the caller graph for this function:

static double blastzScoreToNcbiExpectation

(

int

bzScore

)

[static]

Definition at line 113 of file blastOut.c.

Referenced by ncbiBlastOut(), tabBlastOut(), and xmlBlastOut().

{
double bits = bzScore * 0.0205;
double logProb = -bits*log(2);
return 3.0e9 * exp(logProb);
}

Here is the caller graph for this function:

static int blastzScoreToNcbiScore

(

int

bzScore

)

[static]

Definition at line 107 of file blastOut.c.

References round.

Referenced by xmlBlastOut().

{
return round(bzScore * 0.0529);
}

Here is the caller graph for this function:

static double blastzScoreToWuBits	(	int	bzScore,
		boolean	isProt
	)			[static]

Definition at line 78 of file blastOut.c.

References blastzToWublastScore().

Referenced by wuBlastOut().

{
int wuScore = blastzToWublastScore(bzScore);
if (isProt)
    return wuScore * 0.3545;
else
    return wuScore * 0.1553;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static double blastzScoreToWuExpectation	(	int	bzScore,
		double	databaseSize
	)			[static]

Definition at line 91 of file blastOut.c.

Referenced by wuBlastOut().

{
double logProbOne = -log(2) * bzScore / 32.1948;
return databaseSize * exp(logProbOne);
}

Here is the caller graph for this function:

static int blastzToWublastScore

(

int

bzScore

)

[static]

Definition at line 71 of file blastOut.c.

Referenced by blastzScoreToWuBits(), and wuBlastOut().

{
return bzScore/19;
}

Here is the caller graph for this function:

static struct targetHits* bundleIntoTargets

(

struct axtBundle *

abList

)

[static, read]

Definition at line 288 of file blastOut.c.

References AllocVar, axtRef::axt, axtBundle::axtList, cloneString(), hashAdd(), hashFindVal(), newHash(), axt::next, axtBundle::next, slAddHead, and axtBundle::tSize.

Referenced by ncbiBlastOut(), tabBlastOut(), wuBlastOut(), and xmlBlastOut().

{
struct targetHits *targetList = NULL, *target;
struct hash *targetHash = newHash(10);
struct axtBundle *ab;
struct axtRef *ref;

/* Build up a list of targets in database hit by query sorted by
 * score of hits. */
for (ab = abList; ab != NULL; ab = ab->next)
    {
    struct axt *axt;
    for (axt = ab->axtList; axt != NULL; axt = axt->next)
        {
        target = hashFindVal(targetHash, axt->tName);
        if (target == NULL)
            {
            AllocVar(target);
            slAddHead(&targetList, target);
            hashAdd(targetHash, axt->tName, target);
            target->name = cloneString(axt->tName);
            target->size = ab->tSize;
            }
        if (axt->score > target->score)
            target->score = axt->score;
        AllocVar(ref);
        ref->axt = axt;
        slAddHead(&target->axtList, ref);
        }
    }
slSort(&targetList, targetHitsCmpScore);
for (target = targetList; target != NULL; target = target->next)
    slSort(&target->axtList, axtRefCmpScore);

hashFree(&targetHash);
return targetList;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static int calcDigitCount	(	struct axt *	axt,
		int	tSize,
		int	qSize
	)			[static]

Definition at line 213 of file blastOut.c.

References digitsBaseTen(), max, axt::qEnd, axt::qStart, axt::qStrand, axt::tEnd, axt::tStart, and axt::tStrand.

Referenced by blastiodAxtOutput().

{
int tDig, qDig;
if (axt->qStrand == '-')
    qDig = digitsBaseTen(qSize - axt->qStart + 1);
else
    qDig = digitsBaseTen(axt->qEnd);
if (axt->tStrand == '-')
    tDig = digitsBaseTen(tSize - axt->tStart + 1);
else
    tDig = digitsBaseTen(axt->tEnd);
return max(tDig, qDig);
}

Here is the call graph for this function:

Here is the caller graph for this function:

static int countGapOpens	(	char *	a,
		char *	b,
		int	size
	)			[static]

Definition at line 158 of file blastOut.c.

References FALSE, and TRUE.

Referenced by tabBlastOut().

{
int i, count = 0;
boolean inGap = FALSE;
for (i=0; i<size; ++i)
    {
    if (a[i] == '-' || b[i] == '-')
        {
        if (!inGap)
            {
            ++count;
            inGap = TRUE;
            }
        }
    else
        {
        inGap = FALSE;
        }
    }
return count;
}

Here is the caller graph for this function:

static int countGaps	(	char *	a,
		char *	b,
		int	size
	)			[static]

Definition at line 143 of file blastOut.c.

Referenced by tabBlastOut().

{
int count = 0;
int i;
for (i=0; i<size; ++i)
   {
   if (a[i] == '-')
       ++count;
   if (b[i] == '-')
       ++count;
   }
return count;
}

Here is the caller graph for this function:

static int countMatches	(	char *	a,
		char *	b,
		int	size
	)			[static]

Definition at line 132 of file blastOut.c.

Referenced by ncbiBlastOut(), tabBlastOut(), and wuBlastOut().

{
int count = 0;
int i;
for (i=0; i<size; ++i)
    if (toupper(a[i]) == toupper(b[i]))
        ++count;
return count;
}

Here is the caller graph for this function:

static int countPositives	(	char *	a,
		char *	b,
		int	size
	)			[static]

Definition at line 182 of file blastOut.c.

References axtScoreSchemeProteinDefault(), and ss.

Referenced by wuBlastOut().

{
int count = 0;
int i;
struct axtScoreScheme *ss = axtScoreSchemeProteinDefault();
for (i=0; i<size; ++i)
    {
    if (ss->matrix[(int)a[i]][(int)b[i]] > 0)
        ++count;
    }
return count;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static double expectationToProbability

(

double

e

)

[static]

Definition at line 121 of file blastOut.c.

Referenced by wuBlastOut().

{
if (e < 0.999)
    return e;
else
    return 0.999;
}

Here is the caller graph for this function:

static char* nameForStrand

(

char

strand

)

[static]

Definition at line 328 of file blastOut.c.

Referenced by wuBlastOut().

{
if (strand == '-')
    return "Minus";
else
    return "Plus";
}

Here is the caller graph for this function:

static void ncbiBlastOut	(	struct axtBundle *	abList,
		int	queryIx,
		boolean	isProt,
		FILE *	f,
		char *	databaseName,
		int	databaseSeqCount,
		double	databaseLetterCount,
		char *	ourId,
		double	minIdentity
	)			[static]

Definition at line 483 of file blastOut.c.

References axtBundle::axtList, blastzScoreToNcbiBits(), blastzScoreToNcbiExpectation(), bundleIntoTargets(), countMatches(), axt::frame, ncbiPrintE(), targetHits::next, progType(), axt::qName, axtBundle::qSize, axt::qSym, round, axt::score, sprintLongWithCommas(), axt::symCount, TRUE, and axt::tSym.

Referenced by axtBlastOut().

{
char asciiNum[32];
struct targetHits *targetList = NULL, *target;
char *queryName;
int querySize = abList->qSize;
boolean isTranslated = (abList->axtList->frame != 0);

/* Print out stuff that doesn't depend on query or database. */
if (ourId == NULL)
    ourId = "axtBlastOut";
fprintf(f, "%s 2.2.11 [%s]\n", progType(isProt, abList, TRUE), ourId);
fprintf(f, "\n");
fprintf(f, "Reference:  Kent, WJ. (2002) BLAT - The BLAST-like alignment tool\n");
fprintf(f, "\n");

/* Print query and database info. */
queryName = abList->axtList->qName;
fprintf(f, "Query= %s\n", queryName);
fprintf(f, "         (%d letters)\n", abList->qSize);
fprintf(f, "\n");
fprintf(f, "Database: %s \n",  databaseName);
sprintLongWithCommas(asciiNum, databaseLetterCount);
fprintf(f, "           %d sequences; %s total letters\n",  databaseSeqCount, asciiNum);
fprintf(f, "\n");
fprintf(f, "Searching.done\n");

targetList = bundleIntoTargets(abList);

/* Print out summary of hits. */
fprintf(f, "                                                                 Score    E\n");
fprintf(f, "Sequences producing significant alignments:                      (bits) Value\n");
fprintf(f, "\n");
for (target = targetList; target != NULL; target = target->next)
    {
    struct axtRef *ref;
    struct axt *axt;
    int matches;
    double identity, expectation;
    int bit;
    
    for (ref = target->axtList; ref != NULL; ref = ref->next)
        {
        axt = ref->axt;
        
        matches = countMatches(axt->qSym, axt->tSym, axt->symCount);
        identity = round(100.0 * matches / axt->symCount);
        /* skip output if minIdentity not reached */
        if (identity < minIdentity) continue;
    
        bit = blastzScoreToNcbiBits(axt->score);
        expectation = blastzScoreToNcbiExpectation(axt->score);
        fprintf(f, "%-67s  %4d   ", target->name, bit);
        ncbiPrintE(f, expectation);
        fprintf(f, "\n");
        }
    }
fprintf(f, "\n");

/* Print out details on each target. */
for (target = targetList; target != NULL; target = target->next)
    {
    struct axtRef *ref;
    struct axt *axt;
    int matches, gaps;
    char *oldName;
    
    int ii = 0;
    double identity;
    oldName = strdup("");

    for (ref = target->axtList; ref != NULL; ref = ref->next)
        {
        ii++;
        axt = ref->axt;
        
        matches = countMatches(axt->qSym, axt->tSym, axt->symCount);
        identity = round(100.0 * matches / axt->symCount);
        
        /* skip output if minIdentity not reached */
        if (identity < minIdentity) continue;
        
        /* print target sequence name and length only once */ 
        if (!sameWord(oldName, target->name))
            {
            fprintf(f, "\n\n>%s \n", target->name);
            fprintf(f, "          Length = %d\n", target->size);
            oldName = strdup(target->name);
            }

        fprintf(f, "\n");
        fprintf(f, " Score = %d bits (%d), Expect = ",
             blastzScoreToNcbiBits(axt->score),
             blastzScoreToNcbiScore(axt->score));
        ncbiPrintE(f, blastzScoreToNcbiExpectation(axt->score));
        fprintf(f, "\n");
        
        if (isProt)
            {
            int positives = countPositives(axt->qSym, axt->tSym, axt->symCount);
            gaps = countGaps(axt->qSym, axt->tSym, axt->symCount);
            fprintf(f, " Identities = %d/%d (%d%%),",
                 matches, axt->symCount, round(100.0 * matches / axt->symCount));
            fprintf(f, " Positives = %d/%d (%d%%),",
                 positives, axt->symCount, round(100.0 * positives / axt->symCount));
            fprintf(f, " Gaps = %d/%d (%d%%)\n",
                 gaps, axt->symCount, round(100.0 * gaps / axt->symCount));
            if (axt->frame != 0) 
                fprintf(f, " Frame = %c%d\n", axt->tStrand, axt->frame);
            /* set the special global variable, answer_for_kg.  
               This is needed for Known Genes track building.  Fan 1/21/03 */
            answer_for_kg=axt->symCount - matches;
            }
        else
            {
            fprintf(f, " Identities = %d/%d (%d%%)\n",
                 matches, axt->symCount, round(100.0 * matches / axt->symCount));
            fprintf(f, " Strand = %s / %s\n", nameForStrand(axt->qStrand),
                nameForStrand(axt->tStrand));
            }
        fprintf(f, "\n");
        blastiodAxtOutput(f, axt, target->size, querySize, 60, isProt, isTranslated);
        }
    }

fprintf(f, "  Database: %s\n", databaseName);

/* Cleanup time. */
targetHitsFreeList(&targetList);
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void ncbiPrintE	(	FILE *	f,
		double	e
	)			[static]

Definition at line 462 of file blastOut.c.

References safef().

Referenced by ncbiBlastOut().

{
if (e <= 0.0)
    fprintf(f, "0.0");
else if (e <= 1.0e-100)
    {
    char buf[256], *s;
    safef(buf, sizeof(buf), "%e", e);
    s = strchr(buf, 'e');
    if (s == NULL)
        fprintf(f, "0.0");
    else
        fprintf(f, "%s", s);
    }
else
    fprintf(f, "%1.0e", e);
}

Here is the call graph for this function:

Here is the caller graph for this function:

static int plusStrandPos	(	int	pos,
		int	size,
		char	strand,
		boolean	isEnd
	)			[static]

Definition at line 196 of file blastOut.c.

Referenced by blastiodAxtOutput().

{
if (strand == '-')
    {
    pos = size - pos;
    if (isEnd)
       ++pos;
    }
else
    {
    if (!isEnd)
        ++pos;
    }
return pos;
}

Here is the caller graph for this function:

static void printAxtTargetBlastTab	(	FILE *	f,
		struct axt *	axt,
		int	targetSize
	)			[static]

Definition at line 700 of file blastOut.c.

References axt::qStrand, reverseIntRange(), axt::tEnd, axt::tStart, and axt::tStrand.

Referenced by tabBlastOut().

{
int s = axt->tStart, e = axt->tEnd;
if (axt->tStrand == '-')
    reverseIntRange(&s, &e, targetSize);
if (axt->tStrand == axt->qStrand)
    {
    fprintf(f, "%d\t", s+1);
    fprintf(f, "%d\t", e);
    }
else
    {
    fprintf(f, "%d\t", e);
    fprintf(f, "%d\t", s+1);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static char* progType	(	boolean	isProt,
		struct axtBundle *	ab,
		boolean	isUpper
	)			[static]

Definition at line 337 of file blastOut.c.

References axtBundle::axtList, and axt::frame.

Referenced by ncbiBlastOut(), wuBlastOut(), and xmlBlastOut().

{
if (!isProt)
    return isUpper ? "BLASTN" : "blastn";
else
    {
    if (ab->axtList->frame != 0)
        return isUpper ? "TBLASTN" : "tblastn";
    else
        return isUpper ? "BLASTP" : "blastp";
    }
}

Here is the caller graph for this function:

static void tabBlastOut	(	struct axtBundle *	abList,
		int	queryIx,
		boolean	isProt,
		FILE *	f,
		char *	databaseName,
		int	databaseSeqCount,
		double	databaseLetterCount,
		char *	ourId,
		boolean	withComment
	)			[static]

Definition at line 718 of file blastOut.c.

References axtBundle::axtList, blastzScoreToNcbiBits(), blastzScoreToNcbiExpectation(), bundleIntoTargets(), countGapOpens(), countGaps(), countMatches(), gfVersion, targetHits::next, printAxtTargetBlastTab(), axt::qEnd, axt::qName, axtBundle::qSize, axt::qStart, axt::qStrand, axt::qSym, reverseIntRange(), axt::score, axt::symCount, axt::tName, and axt::tSym.

Referenced by axtBlastOut().

{
char *queryName = abList->axtList->qName;
int querySize = abList->qSize;
struct targetHits *targetList = NULL, *target;

if (withComment)
    {
    char * rcsDate = "$Date: 2006/03/10 17:43:36 $";
    char dateStamp[11];
    strncpy (dateStamp, rcsDate+7, 10);
    dateStamp[10] = 0;
    fprintf(f, "# BLAT %s [%s]\n", gfVersion, dateStamp);
    fprintf(f, "# Query: %s\n", queryName);
    fprintf(f, "# Database: %s\n", databaseName);
    fprintf(f, "%s\n", 
        "# Fields: Query id, Subject id, % identity, alignment length, "
        "mismatches, gap openings, q. start, q. end, s. start, s. end, "
        "e-value, bit score");
    }

/* Print out details on each target. */
targetList = bundleIntoTargets(abList);
for (target = targetList; target != NULL; target = target->next)
    {
    struct axtRef *ref;
    for (ref = target->axtList; ref != NULL; ref = ref->next)
        {
        struct axt *axt = ref->axt;
        int matches = countMatches(axt->qSym, axt->tSym, axt->symCount);
        int gaps = countGaps(axt->qSym, axt->tSym, axt->symCount);
        int gapOpens = countGapOpens(axt->qSym, axt->tSym, axt->symCount);
        fprintf(f, "%s\t", axt->qName);
        fprintf(f, "%s\t", axt->tName);
        fprintf(f, "%.2f\t", 100.0 * matches/axt->symCount);
        fprintf(f, "%d\t", axt->symCount);
        fprintf(f, "%d\t", axt->symCount - matches - gaps);
        fprintf(f, "%d\t", gapOpens);
        if (axt->qStrand == '-')
            {
            int s = axt->qStart, e = axt->qEnd;
            reverseIntRange(&s, &e, querySize);
            fprintf(f, "%d\t", s+1);
            fprintf(f, "%d\t", e);
            printAxtTargetBlastTab(f, axt, target->size);
            }
        else
            {
            fprintf(f, "%d\t", axt->qStart + 1);
            fprintf(f, "%d\t", axt->qEnd);
            printAxtTargetBlastTab(f, axt, target->size);
            }
        fprintf(f, "%3.1e\t", blastzScoreToNcbiExpectation(axt->score));
        fprintf(f, "%d.0\n", blastzScoreToNcbiBits(axt->score));
        }
    }

/* Cleanup time. */
targetHitsFreeList(&targetList);
}

Here is the call graph for this function:

Here is the caller graph for this function:

static int targetHitsCmpScore	(	const void *	va,
		const void *	vb
	)			[static]

Definition at line 62 of file blastOut.c.

References targetHits::score.

{
const struct targetHits *a = *((struct targetHits **)va);
const struct targetHits *b = *((struct targetHits **)vb);

return b->score - a->score;
}

static void targetHitsFree

(

struct targetHits **

pObj

)

[static]

Definition at line 36 of file blastOut.c.

References targetHits::axtList, freeMem(), freez(), targetHits::name, and slFreeList().

Referenced by targetHitsFreeList().

{
struct targetHits *obj = *pObj;
if (obj != NULL)
    {
    freeMem(obj->name);
    slFreeList(&obj->axtList);
    freez(pObj);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void targetHitsFreeList

(

struct targetHits **

pList

)

[static]

Definition at line 48 of file blastOut.c.

References targetHits::next, and targetHitsFree().

Referenced by wuBlastOut().

{
struct targetHits *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    targetHitsFree(&el);
    }
*pList = NULL;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void wuBlastOut	(	struct axtBundle *	abList,
		int	queryIx,
		boolean	isProt,
		FILE *	f,
		char *	databaseName,
		int	databaseSeqCount,
		double	databaseLetterCount,
		char *	ourId
	)			[static]

Definition at line 351 of file blastOut.c.

References axtRef::axt, axtBundle::axtList, blastiodAxtOutput(), blastzScoreToWuBits(), blastzScoreToWuExpectation(), blastzToWublastScore(), bundleIntoTargets(), countMatches(), countPositives(), expectationToProbability(), FALSE, axt::frame, nameForStrand(), axtRef::next, targetHits::next, progType(), axt::qName, axtBundle::qSize, axt::qStrand, axt::qSym, round, axt::score, slCount(), sprintLongWithCommas(), axt::symCount, targetHitsFreeList(), TRUE, axt::tStrand, and axt::tSym.

Referenced by axtBlastOut().

{
char asciiNum[32];
struct targetHits *targetList = NULL, *target;
char *queryName;
int isRc;
int querySize = abList->qSize;
boolean isTranslated = (abList->axtList->frame != 0);

/* Print out stuff that doesn't depend on query or database. */
if (ourId == NULL)
    ourId = "axtBlastOut";
fprintf(f, "%s 2.0MP-WashU [%s]\n", progType(isProt, abList, TRUE), ourId);
fprintf(f, "\n");
fprintf(f, "Copyright (C) 2000-2002 Jim Kent\n");
fprintf(f, "All Rights Reserved\n");
fprintf(f, "\n");
fprintf(f, "Reference:  Kent, WJ. (2002) BLAT - The BLAST-like alignment tool\n");
fprintf(f, "\n");
if (!isProt)
    {
    fprintf(f, "Notice:  this program and its default parameter settings are optimized to find\n");
    fprintf(f, "nearly identical sequences very rapidly.  For slower but more sensitive\n");
    fprintf(f, "alignments please use other methods.\n");
    fprintf(f, "\n");
    }

/* Print query and database info. */
queryName = abList->axtList->qName;
fprintf(f, "Query=  %s\n", queryName);
fprintf(f, "        (%d letters; record %d)\n", abList->qSize, queryIx);
fprintf(f, "\n");
fprintf(f, "Database:  %s\n",  databaseName);
sprintLongWithCommas(asciiNum, databaseLetterCount);
fprintf(f, "           %d sequences; %s total letters\n",  databaseSeqCount, asciiNum);
fprintf(f, "Searching....10....20....30....40....50....60....70....80....90....100%% done\n");
fprintf(f, "\n");

targetList = bundleIntoTargets(abList);

/* Print out summary of hits. */
fprintf(f, "                                                                     Smallest\n");
fprintf(f, "                                                                       Sum\n");
fprintf(f, "                                                              High  Probability\n");
fprintf(f, "Sequences producing High-scoring Segment Pairs:              Score  P(N)      N\n");
fprintf(f, "\n");
for (target = targetList; target != NULL; target = target->next)
    {
    double expectation = blastzScoreToWuExpectation(target->score, databaseLetterCount);
    double p = expectationToProbability(expectation);
    fprintf(f, "%-61s %4d  %8.1e %2d\n", target->name, 
        blastzToWublastScore(target->score), p, slCount(target->axtList));
    }

/* Print out details on each target. */
for (target = targetList; target != NULL; target = target->next)
    {
    fprintf(f, "\n\n>%s\n", target->name);
    fprintf(f, "        Length = %d\n", target->size);
    fprintf(f, "\n");
    for (isRc=0; isRc <= 1; ++isRc)
        {
        boolean saidStrand = FALSE;
        char strand = (isRc ? '-' : '+');
        char *strandName = nameForStrand(strand);
        struct axtRef *ref;
        struct axt *axt;
        for (ref = target->axtList; ref != NULL; ref = ref->next)
            {
            axt = ref->axt;
            if (axt->qStrand == strand)
                {
                int matches = countMatches(axt->qSym, axt->tSym, axt->symCount);
                int positives = countPositives(axt->qSym, axt->tSym, axt->symCount);
                if (!saidStrand)
                    {
                    saidStrand = TRUE;
                    if (!isProt)
                        fprintf(f, "  %s Strand HSPs:\n\n", strandName);
                    }
                fprintf(f, " Score = %d (%2.1f bits), Expect = %5.1e, P = %5.1e\n",
                     blastzToWublastScore(axt->score), 
                     blastzScoreToWuBits(axt->score, isProt),
                     blastzScoreToWuExpectation(axt->score, databaseLetterCount),
                     blastzScoreToWuExpectation(axt->score, databaseLetterCount));
                fprintf(f, " Identities = %d/%d (%d%%), Positives = %d/%d (%d%%)",
                     matches, axt->symCount, round(100.0 * matches / axt->symCount),
                     positives, axt->symCount, round(100.0 * positives / axt->symCount));
                if (isProt)
                    {
                    if (axt->frame != 0)
                        fprintf(f, ", Frame = %c%d", axt->tStrand, axt->frame);
                    fprintf(f, "\n");
                    }
                else
                    fprintf(f, ", Strand = %s / Plus\n", strandName);
                fprintf(f, "\n");
                blastiodAxtOutput(f, axt, target->size, querySize, 60, isProt, isTranslated);
                }
            }
        }
    }

/* Cleanup time. */
targetHitsFreeList(&targetList);
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void xmlBlastOut	(	struct axtBundle *	abList,
		int	queryIx,
		boolean	isProt,
		FILE *	f,
		char *	databaseName,
		int	databaseSeqCount,
		double	databaseLetterCount,
		char *	ourId
	)			[static]

Definition at line 617 of file blastOut.c.

References axtBundle::axtList, blastzScoreToNcbiBits(), blastzScoreToNcbiExpectation(), blastzScoreToNcbiScore(), bundleIntoTargets(), FALSE, targetHits::next, progType(), axt::qEnd, axt::qName, axtBundle::qSize, axt::qStart, axt::score, axt::tEnd, and axt::tStart.

Referenced by axtBlastOut().

{
char *queryName = abList->axtList->qName;
int querySize = abList->qSize;
int hitNum = 0;
struct targetHits *targetList = NULL, *target;

if (ourId == NULL)
    ourId = "axtBlastOut";
fprintf(f, "<?xml version=\"1.0\"?>\n");
fprintf(f, "<!DOCTYPE BlastOutput PUBLIC \"-//NCBI//NCBI BlastOutput/EN\" \"NCBI_BlastOutput.dtd\">\n");
fprintf(f, "<BlastOutput>\n");
fprintf(f, "  <BlastOutput_program>%s</BlastOutput_program>\n", 
        progType(isProt, abList, FALSE));
fprintf(f, "  <BlastOutput_version>%s 2.2.4 [%s]</BlastOutput_version>\n",
        progType(isProt, abList, FALSE), ourId);
fprintf(f, "  <BlastOutput_reference>~Reference: Kent, WJ. (2002) BLAT - The BLAST-like alignment tool</BlastOutput_reference>\n");
fprintf(f, "  <BlastOutput_db>%s</BlastOutput_db>\n", databaseName);
fprintf(f, "  <BlastOutput_query-ID>%d</BlastOutput_query-ID>\n", queryIx);
fprintf(f, "  <BlastOutput_query-def>%s</BlastOutput_query-def>\n", queryName);
fprintf(f, "  <BlastOutput_query-len>%d</BlastOutput_query-len>\n", querySize);

if (isProt)
    {
    fprintf(f, "  <BlastOutput_param>\n");
    fprintf(f, "    <Parameters_matrix>BLOSUM62</Parameters_matrix>\n");
    fprintf(f, "    <Parameters_expect>0.001</Parameters_expect>\n");
    fprintf(f, "    <Parameters_expect>10</Parameters_expect>\n");
    fprintf(f, "    <Parameters_gap-extend>1</Parameters_gap-extend>\n");
    fprintf(f, "  </BlastOutput_param>\n");
    }

fprintf(f, "  <BlastOutput_iterations>\n");
fprintf(f, "    <Iteration>\n");
fprintf(f, "      <Iteration_iter-num>1</Iteration_iter-num>\n");
fprintf(f, "      <Iteration_hits>\n");

/* Print out details on each target. */
targetList = bundleIntoTargets(abList);
for (target = targetList; target != NULL; target = target->next)
    {
    struct axtRef *ref;
    fprintf(f, "      <hit>\n");
    fprintf(f, "        <Hit_num>%d</Hit_num>\n", hitNum);
    fprintf(f, "        <Hit_id>%s</Hit_id>\n", target->name);
    fprintf(f, "        <Hit_accession>%s</Hit_accession>\n", target->name);
    fprintf(f, "        <Hit_len>%d</Hit_len>\n", target->size);
    fprintf(f, "        <Hit_hsps>\n");
    for (ref = target->axtList; ref != NULL; ref = ref->next)
        {
        struct axt *axt = ref->axt;
        int hspIx = 0;
        fprintf(f, "        <Hsp>\n");
        fprintf(f, "          <Hsp_num>%d</Hsp_num>\n", ++hspIx);
        fprintf(f, "          <Hsp_bit-score>%d</Hsp_bit-score>\n", 
                blastzScoreToNcbiBits(axt->score));
        fprintf(f, "          <Hsp_score>%d</Hsp_score>\n",
                blastzScoreToNcbiScore(axt->score));
        fprintf(f, "          <Hsp_evalue>%f</Hsp_evalue>\n",
                blastzScoreToNcbiExpectation(axt->score));
        fprintf(f, "          <Hsp_query-from>%d</Hsp_query-from>\n", 
                axt->qStart+1);
        fprintf(f, "          <Hsp_query-to>%d</Hsp_query-to>\n", axt->qEnd);
        fprintf(f, "          <Hsp_hit-from>%d</Hsp_hit-from>\n", 
                axt->tStart+1);
        fprintf(f, "          <Hsp_hit-to>%d</Hsp_hit-to>\n", axt->tEnd);
        fprintf(f, "        </Hsp>\n");
        }

    fprintf(f, "        </Hit_hsps>\n");
    }

fprintf(f, "      </Iteration_hits>\n");
fprintf(f, "    </Iteration>\n");
fprintf(f, "  </BlastOutput_iterations>\n");
fprintf(f, "</BlastOutput>\n");
}

Here is the call graph for this function:

Here is the caller graph for this function:

---

Variable Documentation

int answer_for_kg

Definition at line 482 of file blastOut.c.

char const rcsid[] = "$Id: blastOut.c,v 1.26 2006/03/10 17:43:36 angie Exp $" [static]

Definition at line 9 of file blastOut.c.

---