lib/blastParse.c File Reference

#include "common.h"
#include "dystring.h"
#include "linefile.h"
#include "dnautil.h"
#include "blastParse.h"
#include "verbose.h"

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Defines
#define	TRACE_LEVEL   3
#define	DUMP_LEVEL   4
Functions
blastFile *	blastFileReadAll (char *fileName)
static void	bfError (struct blastFile *bf, char *message)
static void	bfUnexpectedEof (struct blastFile *bf)
static void	bfSyntax (struct blastFile *bf)
static char *	bfNextLine (struct blastFile *bf)
static boolean	bfSkipBlankLines (struct blastFile *bf)
static char *	bfNeedNextLine (struct blastFile *bf)
static char *	bfSearchForLine (struct blastFile *bf, char *start)
static void	bfBadHeader (struct blastFile *bf)
blastFile *	blastFileOpenVerify (char *fileName)
void	decomma (char *s)
static void	parseQueryLines (struct blastFile *bf, char *line, struct blastQuery *bq)
static void	parseDatabaseLines (struct blastFile *bf, char *line, struct blastQuery *bq)
blastQuery *	blastFileNextQuery (struct blastFile *bf)
blastGappedAli *	blastFileNextGapped (struct blastFile *bf, struct blastQuery *bq)
static int	getStrand (struct blastFile *bf, char *strand)
static boolean	nextBlockLine (struct blastFile *bf, char **retLine)
double	evalToDouble (char *s)
static void	parseBlockLine (struct blastFile *bf, int *startRet, int *endRet, struct dyString *seq)
static struct blastBlock *	nextBlock (struct blastFile *bf, struct blastQuery *bq, struct blastGappedAli *bga, boolean *skipRet)
blastBlock *	blastFileNextBlock (struct blastFile *bf, struct blastQuery *bq, struct blastGappedAli *bga)
void	blastFileFree (struct blastFile **pBf)
void	blastFileFreeList (struct blastFile **pList)
void	blastQueryFree (struct blastQuery **pBq)
void	blastQueryFreeList (struct blastQuery **pList)
void	blastGappedAliFree (struct blastGappedAli **pBga)
void	blastGappedAliFreeList (struct blastGappedAli **pList)
void	blastBlockFree (struct blastBlock **pBb)
void	blastBlockFreeList (struct blastBlock **pList)
void	blastBlockPrint (struct blastBlock *bb, FILE *out)
void	blastGappedAliPrint (struct blastGappedAli *ba, FILE *out)
void	blastQueryPrint (struct blastQuery *bq, FILE *out)

---

Define Documentation

#define DUMP_LEVEL   4

Definition at line 11 of file blastParse.c.

Referenced by blastFileNextQuery().

#define TRACE_LEVEL   3

Definition at line 10 of file blastParse.c.

Referenced by bfNextLine(), blastFileNextGapped(), blastFileNextQuery(), and nextBlock().

---

Function Documentation

static void bfBadHeader

(

struct blastFile *

bf

)

[static]

Definition at line 101 of file blastParse.c.

References bfError().

Referenced by blastFileOpenVerify().

{
bfError(bf, "Bad first line\nShould be something like:\n"
            "BLASTN 2.0.11 [Jan-20-2000]");
}

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static void bfError	(	struct blastFile *	bf,
		char *	message
	)			[static]

Definition at line 29 of file blastParse.c.

References errAbort(), blastFile::fileName, blastFile::lf, and lineFile::lineIx.

Referenced by bfBadHeader(), bfSyntax(), blastFileNextGapped(), getStrand(), nextBlock(), parseDatabaseLines(), and parseQueryLines().

{
errAbort("%s\nLine %d of %s", message, 
        bf->lf->lineIx, bf->fileName);
}

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static char* bfNeedNextLine

(

struct blastFile *

bf

)

[static]

Definition at line 79 of file blastParse.c.

References bfNextLine(), and bfUnexpectedEof().

Referenced by blastFileNextGapped(), blastFileNextQuery(), blastFileOpenVerify(), nextBlock(), parseBlockLine(), parseDatabaseLines(), and parseQueryLines().

{
char *line = bfNextLine(bf);
if (line == NULL)
    bfUnexpectedEof(bf);
return line;
}

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static char* bfNextLine

(

struct blastFile *

bf

)

[static]

Definition at line 48 of file blastParse.c.

References blastFile::lf, lineFileNext(), TRACE_LEVEL, and verbose().

Referenced by bfNeedNextLine(), bfSearchForLine(), bfSkipBlankLines(), blastFileNextGapped(), and nextBlockLine().

{
char *line = NULL;
if (lineFileNext(bf->lf, &line, NULL))
    {
    verbose(TRACE_LEVEL, "=> %s\n", line);
    return line;
    }
else
    {
    verbose(TRACE_LEVEL, "=> EOF\n");
    return NULL;
    }
}

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static char* bfSearchForLine	(	struct blastFile *	bf,
		char *	start
	)			[static]

Definition at line 88 of file blastParse.c.

References bfNextLine(), and startsWith().

Referenced by blastFileNextQuery().

{
for (;;)
    {
    char *line = bfNextLine(bf);
    if (line == NULL)
        return NULL;
    if (startsWith(start, line))
        return line;
    }
}

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static boolean bfSkipBlankLines

(

struct blastFile *

bf

)

[static]

Definition at line 64 of file blastParse.c.

References bfNextLine(), FALSE, blastFile::lf, lineFileReuse(), skipLeadingSpaces(), and TRUE.

Referenced by blastFileNextGapped().

{
char *line = NULL;
while ((line = bfNextLine(bf)) != NULL)
    {
    if (skipLeadingSpaces(line)[0] != '\0')
        {
        lineFileReuse(bf->lf);
        return TRUE;
        }
    }
return FALSE; /* EOF */
}

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static void bfSyntax

(

struct blastFile *

bf

)

[static]

Definition at line 42 of file blastParse.c.

References bfError().

Referenced by nextBlock(), and parseBlockLine().

{
bfError(bf, "Can't cope with BLAST output syntax");
}

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static void bfUnexpectedEof

(

struct blastFile *

bf

)

[static]

Definition at line 36 of file blastParse.c.

References errAbort(), and blastFile::fileName.

Referenced by bfNeedNextLine(), and blastFileNextQuery().

{
errAbort("Unexpected end of file in %s\n", bf->fileName);
}

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void blastBlockFree

(

struct blastBlock **

pBb

)

Definition at line 694 of file blastParse.c.

References freeMem(), freez(), blastBlock::qSym, and blastBlock::tSym.

Referenced by blastBlockFreeList(), and nextBlock().

{
struct blastBlock *bb = *pBb;
if (bb != NULL)
    {
    freeMem(bb->qSym);
    freeMem(bb->tSym);
    freez(pBb);
    }
}

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void blastBlockFreeList

(

struct blastBlock **

pList

)

Definition at line 706 of file blastParse.c.

References blastBlockFree(), and blastBlock::next.

Referenced by blastGappedAliFree().

{
struct blastBlock *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    blastBlockFree(&el);
    }
*pList = NULL;
}

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void blastBlockPrint	(	struct blastBlock *	bb,
		FILE *	out
	)

Definition at line 718 of file blastParse.c.

References blastBlock::insertCount, blastBlock::matchCount, blastBlock::qEnd, blastBlock::qStart, blastBlock::qSym, blastBlock::tEnd, blastBlock::totalCount, blastBlock::tStart, and blastBlock::tSym.

Referenced by blastGappedAliPrint().

{
fprintf(out, "    blk: %d-%d <=> %d-%d tcnt=%d mcnt=%d icnt=%d\n",
        bb->qStart, bb->qEnd,  bb->tStart, bb->tEnd,
        bb->totalCount, bb->matchCount, bb->insertCount);
fprintf(out, "        Q: %s\n", bb->qSym);
fprintf(out, "        T: %s\n", bb->tSym);
}

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void blastFileFree

(

struct blastFile **

pBf

)

Definition at line 615 of file blastParse.c.

References blastQueryFreeList(), blastFile::buildDate, blastFile::fileName, freeMem(), freez(), blastFile::lf, lineFileClose(), blastFile::program, blastFile::queries, and blastFile::version.

Referenced by blastFileFreeList().

{
struct blastFile *bf = *pBf;
if (bf != NULL)
    {
    lineFileClose(&bf->lf);
    freeMem(bf->fileName);
    freeMem(bf->program);
    freeMem(bf->version);
    freeMem(bf->buildDate);
    blastQueryFreeList(&bf->queries);
    freez(pBf);
    }
}

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void blastFileFreeList

(

struct blastFile **

pList

)

Definition at line 631 of file blastParse.c.

References blastFileFree(), and blastFile::next.

{
struct blastFile *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    blastFileFree(&el);
    }
*pList = NULL;
}

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struct blastBlock* blastFileNextBlock	(	struct blastFile *	bf,
		struct blastQuery *	bq,
		struct blastGappedAli *	bga
	)			[read]

Definition at line 601 of file blastParse.c.

References FALSE, and nextBlock().

Referenced by blastFileNextGapped().

{
struct blastBlock *bb = NULL;
boolean skip = FALSE;

while (((bb = nextBlock(bf, bq, bga, &skip)) == NULL) && skip)
    continue; /* skip to next one */

return bb;
}

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struct blastGappedAli* blastFileNextGapped	(	struct blastFile *	bf,
		struct blastQuery *	bq
	)			[read]

Definition at line 286 of file blastParse.c.

References AllocVar, bfError(), bfNeedNextLine(), bfNextLine(), bfSkipBlankLines(), blastFileNextBlock(), blastGappedAli::blocks, chopLine, cloneString(), decomma(), blastGappedAli::query, sameString, slAddHead, slReverse(), startsWith(), blastGappedAli::targetName, blastGappedAli::targetSize, TRACE_LEVEL, and verbose().

Referenced by blastFileNextQuery().

{
char *line;
char *words[16];
int wordCount;
struct blastGappedAli *bga;
struct blastBlock *bb;
int lenSearch;

verbose(TRACE_LEVEL, "blastFileNextGapped\n");
AllocVar(bga);
bga->query = bq;

/* First line should be query. */
if (!bfSkipBlankLines(bf))
    return NULL;
line = bfNextLine(bf);
if (startsWith("  Database:", line))
    return NULL;
if (line[0] != '>')
    bfError(bf, "Expecting >target");
bga->targetName = cloneString(line+1); 

/* Process something like:
 *      Length = 100000
 * however this follows a possible multi-line description, so be specified
 * and limit how far we can scan
 */
for (lenSearch=0; lenSearch<25; lenSearch++)
        {
        line = bfNeedNextLine(bf);
        wordCount = chopLine(line, words);
        if (wordCount == 3 && sameString(words[0], "Length") &&  sameString(words[1], "=")
            && isdigit(words[2][0]))
                break;
        }
if (lenSearch>=25)
    bfError(bf, "Expecting Length =");
decomma(words[2]);
bga->targetSize = atoi(words[2]);

/* Get all the blocks. */
while ((bb = blastFileNextBlock(bf, bq, bga)) != NULL)
    {
    slAddHead(&bga->blocks, bb);
    }
slReverse(&bga->blocks);
return bga;
}

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struct blastQuery* blastFileNextQuery

(

struct blastFile *

bf

)

[read]

Definition at line 237 of file blastParse.c.

References AllocVar, bfNeedNextLine(), bfSearchForLine(), bfUnexpectedEof(), blastFileNextGapped(), blastQueryPrint(), DUMP_LEVEL, blastQuery::gapped, lineFileReuse(), parseDatabaseLines(), parseQueryLines(), slAddHead, slReverse(), stringIn, TRACE_LEVEL, verbose(), and verboseLevel().

Referenced by blastFileReadAll().

{
char *line;
struct blastQuery *bq;
struct blastGappedAli *bga;
AllocVar(bq);

verbose(TRACE_LEVEL, "blastFileNextQuery\n");

/* find and parse Query= */
line = bfSearchForLine(bf, "Query=");
if (line == NULL)
    return NULL;
parseQueryLines(bf, line, bq);

/* find and parse Database: */
line = bfSearchForLine(bf, "Database:");
if (line == NULL)
    bfUnexpectedEof(bf);
parseDatabaseLines(bf, line, bq);

/* Seek to beginning of first gapped alignment. */
for (;;)
    {
    line = bfNeedNextLine(bf);
    if (line[0] == '>')
        {
        lineFileReuse(bf->lf);
        break;
        }
    if (stringIn("No hits found", line) != NULL)
        break;
    }

/* Read in gapped alignments. */
while ((bga = blastFileNextGapped(bf, bq)) != NULL)
    {
    slAddHead(&bq->gapped, bga);
    }
slReverse(&bq->gapped);
if (verboseLevel() >= DUMP_LEVEL)
    {
    verbose(DUMP_LEVEL, "blastFileNextQuery result:\n");
    blastQueryPrint(bq, stderr);
    }
return bq;
}

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struct blastFile* blastFileOpenVerify

(

char *

fileName

)

[read]

Definition at line 108 of file blastParse.c.

References AllocVar, bfBadHeader(), bfNeedNextLine(), blastFile::buildDate, chopLine, cloneString(), blastFile::fileName, blastFile::lf, lineFileOpen(), blastFile::program, TRUE, blastFile::version, and wildMatch().

Referenced by blastFileReadAll().

{
struct blastFile *bf;
char *line;
char *words[16];
int wordCount;
struct lineFile *lf;

AllocVar(bf);
bf->lf = lf = lineFileOpen(fileName, TRUE);
bf->fileName = cloneString(fileName);

/* Parse first line - something like: */
line = bfNeedNextLine(bf);
wordCount = chopLine(line, words);
if (wordCount < 3)
    bfBadHeader(bf);
bf->program = cloneString(words[0]);
bf->version = cloneString(words[1]);
bf->buildDate = cloneString(words[2]);
if (!wildMatch("*BLAST*", bf->program))
    bfBadHeader(bf);
if (!isdigit(bf->version[0]))
    bfBadHeader(bf);
if (bf->buildDate[0] != '[')
    bfBadHeader(bf);
return bf;
}

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struct blastFile* blastFileReadAll

(

char *

fileName

)

[read]

Definition at line 13 of file blastParse.c.

References blastFileNextQuery(), blastFileOpenVerify(), blastFile::lf, lineFileClose(), blastFile::queries, slAddHead, and slReverse().

{
struct blastFile *bf;
struct blastQuery *bq;

bf = blastFileOpenVerify(fileName);
while ((bq = blastFileNextQuery(bf)) != NULL)
    {
    slAddHead(&bf->queries, bq);
    }
slReverse(&bf->queries);
lineFileClose(&bf->lf);
return bf;
}

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void blastGappedAliFree

(

struct blastGappedAli **

pBga

)

Definition at line 669 of file blastParse.c.

References blastBlockFreeList(), blastGappedAli::blocks, freeMem(), freez(), and blastGappedAli::targetName.

Referenced by blastGappedAliFreeList().

{
struct blastGappedAli *bga = *pBga;
if (bga != NULL)
    {
    freeMem(bga->targetName);
    blastBlockFreeList(&bga->blocks);
    freez(pBga);
    }
}

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void blastGappedAliFreeList

(

struct blastGappedAli **

pList

)

Definition at line 681 of file blastParse.c.

References blastGappedAliFree(), and blastGappedAli::next.

Referenced by blastQueryFree().

{
struct blastGappedAli *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    blastGappedAliFree(&el);
    }
*pList = NULL;
}

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void blastGappedAliPrint	(	struct blastGappedAli *	ba,
		FILE *	out
	)

Definition at line 728 of file blastParse.c.

References blastBlockPrint(), blastGappedAli::blocks, blastBlock::next, blastQuery::query, blastGappedAli::query, and blastGappedAli::targetName.

Referenced by blastQueryPrint().

{
struct blastBlock *bb;
fprintf(out, "%s <=> %s\n", ba->query->query, ba->targetName);
for (bb = ba->blocks; bb != NULL; bb = bb->next)
    {
    blastBlockPrint(bb, out);
    }
}

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void blastQueryFree

(

struct blastQuery **

pBq

)

Definition at line 643 of file blastParse.c.

References blastGappedAliFreeList(), blastQuery::database, freeMem(), freez(), blastQuery::gapped, and blastQuery::query.

Referenced by blastQueryFreeList().

{
struct blastQuery *bq;
if ((bq = *pBq) != NULL)
    {
    freeMem(bq->query);
    freeMem(bq->database);
    blastGappedAliFreeList(&bq->gapped);
    freez(pBq);
    }
}

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void blastQueryFreeList

(

struct blastQuery **

pList

)

Definition at line 656 of file blastParse.c.

References blastQueryFree(), and blastQuery::next.

Referenced by blastFileFree().

{
struct blastQuery *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    blastQueryFree(&el);
    }
*pList = NULL;
}

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void blastQueryPrint	(	struct blastQuery *	bq,
		FILE *	out
	)

Definition at line 739 of file blastParse.c.

References blastGappedAliPrint(), blastQuery::gapped, and blastGappedAli::next.

Referenced by blastFileNextQuery().

{
struct blastGappedAli *ba;
for (ba = bq->gapped; ba != NULL; ba = ba->next)
    blastGappedAliPrint(ba, out);
}

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void decomma

(

char *

s

)

Definition at line 138 of file blastParse.c.

Referenced by blastFileNextGapped(), parseDatabaseLines(), and parseQueryLines().

{
char *d = s;
char c;

for (;;)
    {
    c = *s++;
    if (c != ',')
        *d++ = c;
    if (c == 0)
        break;
    }
}

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double evalToDouble

(

char *

s

)

Definition at line 370 of file blastParse.c.

References lineFile::buf, and safef().

Referenced by nextBlock().

{
char buf[64];
if (isdigit(s[0]))
    return atof(s);
else
    {
    safef(buf, sizeof(buf), "1.0%s", s);
    return atof(buf);
    }
}

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static int getStrand	(	struct blastFile *	bf,
		char *	strand
	)			[static]

Definition at line 338 of file blastParse.c.

References bfError(), and sameWord.

Referenced by nextBlock().

{
if (sameWord("Plus", strand))
    return 1;
else if (sameWord("Minus", strand))
    return -1;
else
    {
    bfError(bf, "Expecting Plus or Minus after Strand");
    return 0;
    }
}

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static struct blastBlock* nextBlock	(	struct blastFile *	bf,
		struct blastQuery *	bq,
		struct blastGappedAli *	bga,
		boolean *	skipRet
	)			[static, read]

Definition at line 430 of file blastParse.c.

References AllocVar, ArraySize, bfError(), bfNeedNextLine(), bfSyntax(), blastBlockFree(), chopByChar(), chopLine, cloneMem(), dyStringClear, evalToDouble(), FALSE, getStrand(), lineFileReuse(), newDyString(), nextBlockLine(), parseBlockLine(), blastQuery::queryBaseCount, reverseIntRange(), sameWord, startsWith(), dyString::string, dyString::stringSize, blastGappedAli::targetSize, TRACE_LEVEL, TRUE, and verbose().

Referenced by blastFileNextBlock().

{
struct blastBlock *bb;
char *line;
char *words[16];
int wordCount;
char *parts[3];
int partCount;
static struct dyString *qString = NULL, *tString = NULL;

verbose(TRACE_LEVEL,  "blastFileNextBlock\n");
*skipRet = FALSE;

/* Seek until get something like:
 *   Score = 8770 bits (4424), Expect = 0.0
 * or something that looks like we're done with this gapped
 * alignment. */
for (;;)
    {
    if (!nextBlockLine(bf, &line))
        return NULL;
    if (startsWith(" Score", line))
        break;
    }
AllocVar(bb);
bb->gappedAli = bga;
wordCount = chopLine(line, words);
if (wordCount < 8 || !sameWord("Score", words[0]) 
    || !isdigit(words[2][0]) || !(isdigit(words[7][0]) || words[7][0] == 'e')
    || !startsWith("Expect", words[5]))
    {
    bfError(bf, "Expecting something like:\n"
             "Score = 8770 bits (4424), Expect = 0.0");
    }
bb->bitScore = atoi(words[2]);
bb->eVal = evalToDouble(words[7]);

/* Process something like:
 *   Identities = 8320/9618 (86%), Gaps = 3/9618 (0%)
 *             or
 *   Identities = 8320/9618 (86%)
 *             or
 *   Identities = 10/19 (52%), Positives = 15/19 (78%), Frame = +2
 *     (wu-tblastn)
 *
 * Handle weird cases where the is only a `Score' line, with no `Identities'
 * lines by skipping the alignment; they seem line small, junky alignments.
 */
line = bfNeedNextLine(bf);
wordCount = chopLine(line, words);
if (wordCount < 3 || !sameWord("Identities", words[0]))
    {
    if (wordCount > 1 || sameWord("Score", words[0]))
        {
        /* ugly hack to skip block with no identities */
        *skipRet = TRUE;
        blastBlockFree(&bb);
        return NULL;
        }
    bfError(bf, "Expecting identity count");
    }
partCount = chopByChar(words[2], '/', parts, ArraySize(parts));
if (partCount != 2 || !isdigit(parts[0][0]) || !isdigit(parts[1][0]))
    bfSyntax(bf);
bb->matchCount = atoi(parts[0]);
bb->totalCount = atoi(parts[1]);
if (wordCount >= 7 && sameWord("Gaps", words[4]))
    {
    if (!isdigit(words[6][0]))
        bfSyntax(bf);
    bb->insertCount = atoi(words[6]);
    }
if ((wordCount >= 11) && sameWord("Frame", words[8]))
    {
    bb->qStrand = '+';
    bb->tStrand = words[10][0];
    bb->frame = atoi(words[10]);
    }

/* Process something like:
 *     Strand = Plus / Plus (blastn)
 *     Frame = +1           (tblastn)
 *     <blank line>         (blastp)
 * note that wu-tblastn puts frame on Identities line
 */
line = bfNeedNextLine(bf);
wordCount = chopLine(line, words);
if ((wordCount >= 5) && sameWord("Strand", words[0]))
    {
    bb->qStrand = getStrand(bf, words[2]);
    bb->tStrand = getStrand(bf, words[4]);
    }
else if ((wordCount >= 3) && sameWord("Frame", words[0]))
    {
    bb->qStrand = 1;
    bb->tStrand = (words[2][0] == '-') ? -1 : 1;
    bb->frame = atoi(words[2]);
    }
else if (wordCount == 0)
    {
    /* if we didn't parse frame, default it */
    if (bb->qStrand == 0)
        {
        bb->qStrand = '+';
        bb->tStrand = '+';
        }
    }
else
    bfError(bf, "Expecting Strand, Frame or blank line");


/* Process alignment lines.  They come in groups of three
 * separated by a blank line - something like:
 * Query: 26429 taccttgacattcctcagtgtgtcatcatcgttctctcctccaaacggcgagagtccgga 26488
 *              |||||| |||||||||| ||| ||||||||||||||||||||||| || || ||||||||
 * Sbjct: 62966 taccttaacattcctcaatgtttcatcatcgttctctcctccaaatggtgaaagtccgga 63025
 */
bb->qStart = bb->tStart = 0x3fffffff;
bb->qEnd = bb->tEnd = -bb->qStart;
if (qString == NULL)
    {
    qString = newDyString(50000);
    tString = newDyString(50000);
    }
else
    {
    dyStringClear(qString);
    dyStringClear(tString);
    }
for (;;)
    {
    /* Fetch next first line. */
    for (;;)
        {
        if (!nextBlockLine(bf, &line))
            goto DONE;
        if (startsWith(" Score", line))
            {
            lineFileReuse(bf->lf);
            goto DONE;
            }
        if (startsWith("Query:", line))
            break;
        }
    lineFileReuse(bf->lf);
    parseBlockLine(bf, &bb->qStart, &bb->qEnd, qString);

    /* Skip next line. */
    line = bfNeedNextLine(bf);

    /* Fetch target sequence line. */
    parseBlockLine(bf, &bb->tStart, &bb->tEnd, tString);
    }
DONE:

/* convert to [0..n) and move to strand coords if necessary */
bb->qStart--;
if (bb->qStrand < 0)
    reverseIntRange(&bb->qStart, &bb->qEnd, bq->queryBaseCount);
bb->tStart--;
if (bb->tStrand < 0)
    reverseIntRange(&bb->tStart, &bb->tEnd, bga->targetSize);
bb->qSym = cloneMem(qString->string, qString->stringSize+1);
bb->tSym = cloneMem(tString->string, tString->stringSize+1);
return bb;
}

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static boolean nextBlockLine	(	struct blastFile *	bf,
		char **	retLine
	)			[static]

Definition at line 352 of file blastParse.c.

References bfNextLine(), FALSE, blastFile::lf, lineFileReuse(), startsWith(), and TRUE.

Referenced by nextBlock().

{
struct lineFile *lf = bf->lf;
char *line;

*retLine = line = bfNextLine(bf);
if (line == NULL)
    return FALSE;
if (line[0] == '>' || startsWith("Query=", line) || startsWith("  Database:", line))
    {
    lineFileReuse(lf);
    return FALSE;
    }
return TRUE;
}

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static void parseBlockLine	(	struct blastFile *	bf,
		int *	startRet,
		int *	endRet,
		struct dyString *	seq
	)			[static]

Definition at line 386 of file blastParse.c.

References bfNeedNextLine(), bfSyntax(), chopLine, dyStringAppend(), max, min, and sameString.

Referenced by nextBlock().

                                                     :
 *   Query: 26429 taccttgacattcctcagtgtgtcatcatcgttctctcctccaaacggcgagagtccgga 26488
 *
 * also handle broken NCBI tblastn output like:
 *   Sbjct: 1181YYGEQRSTNGQTIQLKTQVFRRFPDDDDESEDHDDPDNAHESPEQEGAEGHFDLHYYENQ 1360
 */
{
char* line = bfNeedNextLine(bf);
int a, b, s, e;
char *words[16];
int wordCount = chopLine(line, words);
if ((wordCount < 3) || (wordCount > 4)
    || !(sameString("Query:", words[0]) || sameString("Sbjct:", words[0])))
    bfSyntax(bf);

/* special handling for broken output */
if (wordCount == 3)
    {
    char *p;
    if (!isdigit(words[1][0]) || !isdigit(words[2][0]))
        bfSyntax(bf);
    a = atoi(words[1]);
    b = atoi(words[2]);
    p = words[1];
    while ((*p != '\0') && (isdigit(*p)))
        p++;
    dyStringAppend(seq, p);
    }
else
    {
    if (!isdigit(words[1][0]) || !isdigit(words[3][0]))
        bfSyntax(bf);
    a = atoi(words[1]);
    b = atoi(words[3]);
    dyStringAppend(seq, words[2]);
    }
s = min(a,b);
e = max(a,b);
*startRet = min(s, *startRet);
*endRet = max(e, *endRet);
}

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static void parseDatabaseLines	(	struct blastFile *	bf,
		char *	line,
		struct blastQuery *	bq
	)			[static]

Definition at line 194 of file blastParse.c.

References bfError(), bfNeedNextLine(), chopLine, cloneString(), blastQuery::database, blastQuery::dbBaseCount, blastQuery::dbSeqCount, decomma(), dyStringAppend(), dyStringClear, dyStringNew, and dyString::string.

Referenced by blastFileNextQuery().

                         :
 * Database: chr22.fa 
 *        977 sequences; 95,550,797 total letters
 */
{
static struct dyString *tmpBuf = NULL;
char *words[16];
int wordCount;
if (bq->database != NULL)
    bfError(bf, "already parse Database:");

if (tmpBuf == NULL)
    tmpBuf = dyStringNew(512);

/* parse something like
 * Database: celegans98
 * some versions of blastp include the absolute path, but
 * then split it across lines.
 */
wordCount = chopLine(line, words);
if (wordCount < 2)
    bfError(bf, "Expecting database name");
dyStringClear(tmpBuf);
dyStringAppend(tmpBuf, words[1]);
while (line = bfNeedNextLine(bf), !isspace(line[0]))
    {
    dyStringAppend(tmpBuf, line);
    }
bq->database = cloneString(tmpBuf->string);

/* Process something like:
 *        977 sequences; 95,550,797 total letters
 */
wordCount = chopLine(line, words);
if (wordCount < 3 || !isdigit(words[0][0]) || !isdigit(words[2][0]))
    bfError(bf, "Expecting database info");
decomma(words[0]);
decomma(words[2]);
bq->dbSeqCount = atoi(words[0]);
bq->dbBaseCount = atoi(words[2]);
}

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static void parseQueryLines	(	struct blastFile *	bf,
		char *	line,
		struct blastQuery *	bq
	)			[static]

Definition at line 154 of file blastParse.c.

References bfError(), bfNeedNextLine(), chopLine, cloneString(), decomma(), blastQuery::query, blastQuery::queryBaseCount, and skipLeadingSpaces().

Referenced by blastFileNextQuery().

{
char *s, *e;
char *words[16];
int wordCount;
if (bq->query != NULL)
    bfError(bf, "already parse Query=");

/* Process something like:
 *    Query= MM39H11    00630     
 */
wordCount = chopLine(line, words);
if (wordCount < 2)
    bfError(bf, "No sequence name in query line");
bq->query = cloneString(words[1]);

for (;;)
    {
    line = bfNeedNextLine(bf);
    s = skipLeadingSpaces(line);
    if (s[0] == '(')
        break;
    }
if (!isdigit(s[1]))
    {
    bfError(bf, "expecting something like:\n"
                "   (45,693 letters)");
    }
s += 1;
if ((e = strchr(s, ' ')) == NULL)
    {
    bfError(bf, "expecting something like:\n"
                "   (45,693 letters)");
    }
*e = 0;
decomma(s);
bq->queryBaseCount = atoi(s);
}

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