src/lib/gff3.c 1.2
1.2 2009/05/17 15:18:03 markd
fixed use of non-posix include
Index: src/lib/gff3.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/gff3.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/lib/gff3.c 22 Apr 2009 16:56:49 -0000 1.1
+++ src/lib/gff3.c 17 May 2009 15:18:03 -0000 1.2
@@ -1,914 +1,914 @@
/*
* Object for accessing GFF3 files
* See GFF3 specification for details of file format:
* http://www.sequenceontology.org/gff3.shtml
*/
#include "common.h"
#include "gff3.h"
-#include <values.h>
+#include <limits.h>
#include "errabort.h"
#include "localmem.h"
#include "hash.h"
#include "linefile.h"
#include "dystring.h"
#include "fa.h"
// FIXME: spec unclear if attributes can be specified multiple times
// FIXME: spec unclear if start/end can be `.'
// FIXME: should spaces be striped from attributes?
// FIXME: chop functions might cause grief by skipping initial separators
static const int gffNumCols = 9;
/* standard attribute names */
char *gff3AttrID = "ID";
char *gff3AttrName = "Name";
char *gff3AttrAlias = "Alias";
char *gff3AttrParent = "Parent";
char *gff3AttrTarget = "Target";
char *gff3AttrGap = "Gap";
char *gff3AttrDerivesFrom = "Derives_from";
char *gff3AttrNote = "Note";
char *gff3AttrDbxref = "Dbxref";
char *gff3AttrOntologyTerm = "Ontology_term";
static void gff3FileErr(struct gff3File *g3f, char *format, ...)
#if defined(__GNUC__)
__attribute__((format(printf, 2, 3)))
#endif
;
static void gff3AnnErr(struct gff3Ann *g3a, char *format, ...)
#if defined(__GNUC__)
__attribute__((format(printf, 2, 3)))
#endif
;
static void vaGff3FileErr(struct gff3File *g3f, char *format, va_list args)
/* Print error message to error file, abort if max errors have been reached */
{
if (g3f->lf != NULL)
fprintf(g3f->errFh, "%s:%d: ", g3f->lf->fileName, g3f->lf->lineIx);
vfprintf(g3f->errFh, format, args);
fprintf(g3f->errFh, "\n");
g3f->errCnt++;
if (g3f->errCnt > g3f->maxErr)
errAbort("GFF3: %d parser errors", g3f->errCnt);
}
static void gff3FileErr(struct gff3File *g3f, char *format, ...)
/* Print error message and abort */
{
va_list args;
va_start(args, format);
vaGff3FileErr(g3f, format, args);
va_end(args);
}
static void gff3AnnErr(struct gff3Ann *g3a, char *format, ...)
/* Print error message abort */
{
va_list args;
va_start(args, format);
vaGff3FileErr(g3a->file, format, args);
va_end(args);
}
static int gff3FileStrToInt(struct gff3File *g3f, char *str)
/* convert a string to an integer */
{
char *end;
long val = strtol(str, &end, 0);
if ((end == str) || (*end != '\0'))
gff3FileErr(g3f, "invalid integer: %s", str);
return (int)val;
}
static float gff3FileStrToFloat(struct gff3File *g3f, char *str)
/* convert a string to a float */
{
char *end;
double val = strtod(str, &end);
if ((end == str) || (*end != '\0'))
gff3FileErr(g3f, "invalid float: %s", str);
return (float)val;
}
static void *gff3FileAlloc(struct gff3File *g3f, size_t size)
/* allocate memory from the memory pool */
{
return lmAlloc(g3f->pool->lm, size);
}
static char *gff3FileCloneStr(struct gff3File *g3f, char *str)
/* allocate memory for a string and copy if */
{
return lmCloneString(g3f->pool->lm, str);
}
static char *gff3FilePooledStr(struct gff3File *g3f, char *str)
/* allocate memory for a string from the shared string pool */
{
return hashStore(g3f->pool, str)->name;
}
static struct slName *gff3FileSlNameNew(struct gff3File *g3f, char *name)
/* allocate slName from the memory pool */
{
return lmSlName(g3f->pool->lm, name);
}
static char **dynChopStringWhite(struct gff3File *g3f, char *str, int minWords, int maxWords, int *numWordsRet, char *desc)
/* dynamic chop string without corrupting it, generate error if expected
* number of words not found. Free return when done. Returns NULL on
* error. */
{
int numWords = chopByWhite(str, NULL, 0);
if ((numWords < minWords) || (numWords > maxWords))
{
gff3FileErr(g3f, "expected %s, got \"%s\"", desc, str);
return NULL;
}
// allocate buffer for both array and string
int wordsBytes = ((numWords+1)*sizeof(char**));
char **words = needMem(wordsBytes+strlen(str)+1);
char *strcp = ((char*)words)+wordsBytes;
strcpy(strcp, str);
chopByWhite(strcp, words, numWords);
words[numWords] = NULL;
if (numWordsRet != NULL)
*numWordsRet = numWords;
return words;
}
struct gff3AttrVals *gff3AnnFindAttr(struct gff3Ann *g3a, char *attr)
/* find a user attribute, or NULL */
{
struct gff3AttrVals *av;
for (av = g3a->attrs; av != NULL; av = av->next)
{
if (sameString(av->attr, attr))
return av;
}
return NULL;
}
static struct gff3AnnRef *gff3AnnRefAlloc(struct gff3Ann *g3a)
/* construct an annotation reference, allocated in the memory pool*/
{
struct gff3AnnRef *ref = gff3FileAlloc(g3a->file, sizeof(struct gff3AnnRef));
ref->ann = g3a;
return ref;
}
static void raiseInvalidEscape(struct gff3Ann *g3a, char *str)
/* raise an error about an invalid escape in a string */
{
gff3AnnErr(g3a, "invalid GFF escape sequence in string: %s", str);
}
static char convertEscape(struct gff3Ann *g3a, char *esc, char *src)
/* convert character at esc, which should start with a `%' and be a string
* in the form `%09' */
{
if (!(isxdigit(esc[1]) && isxdigit(esc[1])))
raiseInvalidEscape(g3a, src);
char num[3], *end;
strncpy(num, esc+1, 2);
num[2] = '\0';
long val = strtol(num, &end, 16);
if ((end == num) || (*end != '\0'))
raiseInvalidEscape(g3a, src);
return (char)val;
}
static void unescapeStr(struct gff3Ann *g3a, char *dest, char *src)
/* remove URL-style escapes from a string. dest need only have enough
* memory to hold src, as unescaping will not grow the string */
{
char *s = src, *d = dest;
while (*s != '\0')
{
if (*s == '%')
{
*d++ = convertEscape(g3a, s, src);
s += 3;
}
else
*d++ = *s++;
}
*d = '\0';
}
static struct slName *unescapeSlName(struct gff3Ann *g3a, char *src)
/* unescape the string and put in an slName object, storing it in memory
* allocated from localmem */
{
struct slName *dest = gff3FileAlloc(g3a->file, sizeof(struct slName)+strlen(src));
unescapeStr(g3a, dest->name, src);
return dest;
}
static char *unescapeStrTmp(struct gff3Ann *g3a, char *src)
/* unescape the string into a tmp buffer. WARNING: return is a static and
* maybe invalidated by calling another unescape function */
{
static struct dyString *buf = NULL; // buffer for tmp copy of unescaped string
if (buf == NULL)
buf = dyStringNew(256);
dyStringBumpBufSize(buf, strlen(src)+1);
unescapeStr(g3a, buf->string, src);
return buf->string;
}
static char *unescapeStrPooled(struct gff3Ann *g3a, char *src)
/* unescape the string and obtain it from localmem */
{
return gff3FilePooledStr(g3a->file, unescapeStrTmp(g3a, src));
}
static char *escapeChar(char c)
/* escape a character. Warning: static return */
{
static char ec[4];
safef(ec, sizeof(ec), "%%%02X", c);
return ec;
}
static boolean isMetaChar(char c)
/* determine if a character is a GFF3 meta character */
{
return ((c == '\t') || (c == '\n') || (c == '\r') || !isprint(c) || (c == ';') || (c == '=') || (c == '&') || (c == ','));
}
static void writeEscaped(char *str, FILE *fh)
/* write a data string to a file, escaping as needed */
{
char *c;
for (c = str; *c != '\0'; c++)
{
if (isMetaChar(*c))
fputs(escapeChar(*c), fh);
else
fputc(*c, fh);
}
}
static char *parseStrand(struct gff3Ann *g3a, char *strand)
/* parse strand into static string, validating it */
{
if (sameString(strand, "."))
return NULL;
else if (sameString(strand, "+"))
return "+";
else if (sameString(strand, "-"))
return "-";
else if (sameString(strand, "?"))
return "?";
else
gff3AnnErr(g3a, "invalid strand: '%s'", strand);
return NULL;
}
static int parsePhase(struct gff3Ann *g3a, char *str)
/* parse phase into a number, validating it */
{
if (sameString(str, "."))
return -1;
int phase = gff3FileStrToInt(g3a->file, str);
if ((phase < 0) || (phase > 2))
gff3AnnErr(g3a, "invalid phase: %d", phase);
return phase;
}
static void parseFields(struct gff3Ann *g3a, char **words)
/* parse the field in an annotation record */
{
g3a->seqid = unescapeStrPooled(g3a, words[0]);
g3a->source = unescapeStrPooled(g3a, words[1]);
g3a->type = unescapeStrPooled(g3a, words[2]);
g3a->start = gff3FileStrToInt(g3a->file, words[3])-1;
g3a->end = gff3FileStrToInt(g3a->file, words[4]);
if (!sameString(words[5], "."))
{
g3a->score = gff3FileStrToFloat(g3a->file, words[5]);
g3a->haveScore = TRUE;
}
g3a->strand = parseStrand(g3a, words[6]);
g3a->phase = parsePhase(g3a, words[7]);
if (sameString(g3a->type, "CDS") && (g3a->phase < 0))
gff3AnnErr(g3a, "CDS feature must have phase");
}
static struct slName *parseAttrVals(struct gff3Ann *g3a, char *attr, char *valsStr)
/* parse an attribute into its values */
{
int i, numVals = chopString(valsStr, ",", NULL, 0);
char **vals = needMem((numVals+1)*sizeof(char**)); // +1 allows for no values
chopString(valsStr, ",", vals, numVals);
struct slName *escVals = NULL;
for (i = 0; i < numVals; i++)
slSafeAddHead(&escVals, unescapeSlName(g3a, vals[i]));
freeMem(vals);
slReverse(&escVals);
return escVals;
}
static void addAttrVals(struct gff3Ann *g3a, char *attr, char *valStr)
/* Add an attribute to the list of attributes. If attribute has already been
* specified, values are merged. Attribute name must already be unescaped,
* attribute values will be split and then unescaped. */
{
struct gff3AttrVals *attrVals = gff3AnnFindAttr(g3a, attr);
if (attrVals == NULL)
{
attrVals = gff3FileAlloc(g3a->file, sizeof(struct gff3AttrVals));
attrVals->attr = gff3FileCloneStr(g3a->file, attr);
slAddHead(&g3a->attrs, attrVals);
}
attrVals->vals = slCat(attrVals->vals, parseAttrVals(g3a, attr, valStr));
}
static void parseAttrVal(struct gff3Ann *g3a, char *attrValsStr)
/* parse one attribute and value from an annotation record */
{
char *eq = strchr(attrValsStr, '=');
if ((eq == NULL) || (eq == attrValsStr))
gff3AnnErr(g3a, "expected name=value: %s", attrValsStr);
char *attr = attrValsStr;
char *vals = eq+1;
*eq = '\0';
unescapeStr(g3a, attr, attr);
addAttrVals(g3a, attr, vals);
}
static void parseAttrs(struct gff3Ann *g3a, char *attrsCol)
/* parse the attribute column in an annotation record */
{
int i, numAttrs = chopString(attrsCol, ";", NULL, 0);
char **attrVals = needMem(numAttrs*sizeof(char**));
chopString(attrsCol, ";", attrVals, numAttrs);
for (i = 0; i < numAttrs; i++)
{
char *av = trimSpaces(attrVals[i]);
if (strlen(av) > 0)
parseAttrVal(g3a, av);
}
freeMem(attrVals);
slReverse(&g3a->attrs);
}
static void checkSingleValAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* validate that an attribute has only one value */
{
if (attrVals->vals->next != NULL)
gff3AnnErr(g3a, "attribute %s must have a single value, found multiple comma-separated values", attrVals->attr);
}
static void parseIDAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the ID attribute */
{
checkSingleValAttr(g3a, attrVals);
char *id = attrVals->vals->name;
struct hashEl *hel = hashStore(g3a->file->byId, id);
if (hel->val != NULL)
gff3AnnErr(g3a, "duplicate annotation record with ID: %s", id);
hel->val = g3a;
g3a->id = id;
}
static void parseNameAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Name attribute */
{
checkSingleValAttr(g3a, attrVals);
g3a->name = attrVals->vals->name;
}
static void parseAliasAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Alias attribute */
{
g3a->aliases = attrVals->vals;
}
static void parseParentAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Parent attribute */
{
g3a->parentIds = attrVals->vals;
}
static void parseTargetAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Target attribute */
{
checkSingleValAttr(g3a, attrVals);
// target_id start end [strand]
int numWords;
char **words = dynChopStringWhite(g3a->file, attrVals->vals->name, 3, 4, &numWords,
"Target attribute in the form \"target_id start end [strand]\"");
if (words == NULL)
return; // got an error
g3a->targetId = gff3FileCloneStr(g3a->file, words[0]);
g3a->targetStart = gff3FileStrToInt(g3a->file, words[1])-1;
g3a->targetEnd = gff3FileStrToInt(g3a->file, words[2]);
if (numWords > 3)
g3a->targetStrand = parseStrand(g3a, words[3]);
freeMem(words);
}
static void parseGapAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Gap attribute */
{
checkSingleValAttr(g3a, attrVals);
g3a->gap = attrVals->vals->name;
}
static void parseDerivesFromAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Derives_from attribute */
{
g3a->derivesFromId = attrVals->vals->name;
}
static void parseNoteAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Note attribute */
{
g3a->notes = attrVals->vals;
}
static void parseDbxrefAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Dbxref attribute */
{
g3a->dbxrefs = attrVals->vals;
}
static void parseOntologyTermAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* parse the Ontology_term attribute */
{
g3a->ontologyTerms = attrVals->vals;
}
static void parseStdAttr(struct gff3Ann *g3a, struct gff3AttrVals *attrVals)
/* Parse one of the standard specified attributes (those starting with upper
* case) into fields. Multiple specifications of an attribute should have been
* merged before calling this function. */
{
if (sameString(attrVals->attr, gff3AttrID))
parseIDAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrName))
parseNameAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrAlias))
parseAliasAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrParent))
parseParentAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrTarget))
parseTargetAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrGap))
parseGapAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrDerivesFrom))
parseDerivesFromAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrNote))
parseNoteAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrDbxref))
parseDbxrefAttr(g3a, attrVals);
else if (sameString(attrVals->attr, gff3AttrOntologyTerm))
parseOntologyTermAttr(g3a, attrVals);
else
gff3AnnErr(g3a, "unknown standard attribute, user defined attributes must start with a lower-case letter: %s", attrVals->attr);
}
static void parseStdAttrs(struct gff3Ann *g3a)
/* parse standard attributes (starting with upper case) into attributes
* have been parsed into attribute list, which would have merged multiply
* specified attributes. */
{
struct gff3AttrVals *av;
for (av = g3a->attrs; av != NULL; av = av->next)
{
if (isupper(av->attr[0]))
parseStdAttr(g3a, av);
}
}
static void parseAnn(struct gff3File *g3f, char *line)
/* parse an annotation line */
{
// extra column to check for too many
char *words[gffNumCols+1];
int numWords = chopString(line, "\t", words, gffNumCols+1);
if (numWords != gffNumCols)
gff3FileErr(g3f, "expected %d tab-separated columns: %s", gffNumCols, line);
struct gff3Ann *g3a = gff3FileAlloc(g3f, sizeof(struct gff3Ann));
g3a->file = g3f;
g3a->lineNum = g3f->lf->lineIx;
parseFields(g3a, words);
parseAttrs(g3a, words[8]);
parseStdAttrs(g3a);
slAddHead(&g3f->anns, g3a);
}
static void writeAttrVals(struct gff3AttrVals *av, FILE *fh)
/* write one attribute and it's values */
{
writeEscaped(av->attr, fh);
fputc('=', fh);
struct slName *val;
for (val = av->vals; val != NULL; val = val->next)
{
if (val != av->vals)
fputc(',', fh);
writeEscaped(val->name, fh);
}
}
static void writeAttrs(struct gff3Ann *g3a, FILE *fh)
/* write annotation record attributes */
{
struct gff3AttrVals *av;
for (av = g3a->attrs; av != NULL; av = av->next)
{
if (av != g3a->attrs)
fputc(';', fh);
writeAttrVals(av, fh);
}
}
static void writeFields(struct gff3Ann *g3a, FILE *fh)
/* write an annotation record fields */
{
writeEscaped(g3a->seqid, fh);
fputc('\t', fh);
writeEscaped(g3a->source, fh);
fputc('\t', fh);
writeEscaped(g3a->type, fh);
fprintf(fh, "\t%d\t%d", g3a->start+1, g3a->end);
fputc('\t', fh);
if (g3a->haveScore)
fprintf(fh, "%g", g3a->score);
else
fputc('.', fh);
fprintf(fh, "\t%c", (g3a->strand != NULL) ? g3a->strand[0] : '.');
fputc('\t', fh);
if (g3a->phase < 0)
fputc('.', fh);
else
fprintf(fh, "%d", g3a->phase);
}
static void writeAnn(struct gff3Ann *g3a, FILE *fh)
/* write an annotation record to the specified file */
{
writeFields(g3a, fh);
fputc('\t', fh);
writeAttrs(g3a, fh);
fputc('\n', fh);
}
static void addFasta(struct gff3File *g3f, char *dna, int size, char *name)
/* add one fasta record */
{
struct dnaSeq *dnaSeq = gff3FileAlloc(g3f, sizeof(struct dnaSeq));
slAddHead(&g3f->seqs, dnaSeq);
struct hashEl *hel = hashAdd(g3f->seqMap, name, dnaSeq);
dnaSeq->name = hel->name;
dnaSeq->dna = gff3FileCloneStr(g3f, dna);
dnaSeq->size = size;
}
static void parseFasta(struct gff3File *g3f)
/* parse fasta records in the file, consumes remainder of file */
{
char *dna, *name;
int size;
g3f->seqMap = hashNew(0);
while (faMixedSpeedReadNext(g3f->lf, &dna, &size, &name))
addFasta(g3f, dna, size, name);
}
static void writeFastas(struct gff3File *g3f, FILE *fh)
/* write fasta records fo the file */
{
if (g3f->seqs != NULL)
{
fputs("##FASTA\n", fh);
struct dnaSeq *seq;
for (seq = g3f->seqs; seq != NULL; seq = seq->next)
faWriteNext(fh, seq->name, seq->dna, seq->size);
}
}
static void parseSequenceRegion(struct gff3File *g3f, char *line)
/* parse ##sequence-region seqid start end */
{
char **words = dynChopStringWhite(g3f, line, 4, 4, NULL,
"\"##sequence-region seqid start end\"");
if (words == NULL)
return; // got an error
struct gff3SeqRegion *sr = gff3FileAlloc(g3f, sizeof(struct gff3SeqRegion));
sr->seqid = gff3FileCloneStr(g3f, words[1]);
sr->start = gff3FileStrToInt(g3f, words[2])-1;
sr->end = gff3FileStrToInt(g3f, words[3]);
if (g3f->seqRegionMap == NULL)
g3f->seqRegionMap = hashNew(0);
struct hashEl *hel = hashStore(g3f->seqRegionMap, sr->seqid);
if (hel->val != NULL)
gff3FileErr(g3f, "duplicate ##sequence-region for %s", sr->seqid);
else
{
hel->val = sr;
slAddHead(&g3f->seqRegions, sr);
}
freeMem(words);
}
static void writeSequenceRegions(struct gff3File *g3f, FILE *fh)
/* parse ##sequence-region metadata */
{
struct gff3SeqRegion *sr;
for (sr = g3f->seqRegions; sr != NULL; sr = sr->next)
fprintf(fh, "##sequence-region %s %d %d\n", sr->seqid, sr->start, sr->end);
}
static void writeSlNameMetas(char *metaName, struct slName *metas, FILE *fh)
/* write meta records stores as slNames */
{
struct slName *m;
for (m = metas; m != NULL; m = m->next)
fprintf(fh, "%s %s\n", metaName, m->name);
}
static void parseFeatureOntology(struct gff3File *g3f, char *line)
/* parse ##feature-ontology URI */
{
char **words = dynChopStringWhite(g3f, line, 2, 2, NULL,
"\"##feature-ontology URI\"");
if (words == NULL)
return; // got an error
slSafeAddHead(&g3f->featureOntologies, gff3FileSlNameNew(g3f, words[1]));
freeMem(words);
}
static void writeFeatureOntologies(struct gff3File *g3f, FILE *fh)
/* parse ##feature-ontology metas */
{
writeSlNameMetas("##feature-ontology", g3f->featureOntologies, fh);
}
static void parseAttributeOntology(struct gff3File *g3f, char *line)
/* parse ##attribute-ontology URI */
{
char **words = dynChopStringWhite(g3f, line, 2, 2, NULL,
"\"##attribute-ontology URI\"");
if (words == NULL)
return; // got an error
slSafeAddHead(&g3f->attributeOntologies, gff3FileSlNameNew(g3f, words[1]));
freeMem(words);
}
static void writeAttributeOntologies(struct gff3File *g3f, FILE *fh)
/* write ##attribute-ontology metas */
{
writeSlNameMetas("##attribute-ontology", g3f->attributeOntologies, fh);
}
static void parseSourceOntology(struct gff3File *g3f, char *line)
/* parse ##source-ontology URI */
{
char **words = dynChopStringWhite(g3f, line, 2, 2, NULL,
"\"##source-ontology URI\"");
if (words == NULL)
return; // got an error
slSafeAddHead(&g3f->sourceOntologies, gff3FileSlNameNew(g3f, words[1]));
freeMem(words);
}
static void writeSourceOntologies(struct gff3File *g3f, FILE *fh)
/* write ##source-ontology metas */
{
writeSlNameMetas("##source-ontology", g3f->sourceOntologies, fh);
}
static void parseSpecies(struct gff3File *g3f, char *line)
/* parse ##species NCBI_Taxonomy_URI */
{
char **words = dynChopStringWhite(g3f, line, 2, 2, NULL,
"\"##species NCBI_Taxonomy_URI\"");
if (words == NULL)
return; // got an error
slSafeAddHead(&g3f->species, gff3FileSlNameNew(g3f, words[1]));
freeMem(words);
}
static void writeSpecies(struct gff3File *g3f, FILE *fh)
/* write ##species NCBI_Taxonomy_URI */
{
writeSlNameMetas("##species", g3f->species, fh);
}
static void parseGenomeBuild(struct gff3File *g3f, char *line)
/* parse ##genome-build source buildName */
{
if (g3f->genomeBuildSource != NULL)
gff3FileErr(g3f, "multiple ##genome-build records");
char **words = dynChopStringWhite(g3f, line, 3, 3, NULL,
"\"##genome-build source buildName\"");
if (words == NULL)
return; // got an error
g3f->genomeBuildSource = gff3FileCloneStr(g3f, words[1]);
g3f->genomeBuildName = gff3FileCloneStr(g3f, words[2]);
freeMem(words);
}
static void writeGenomeBuild(struct gff3File *g3f, FILE *fh)
/* parse ##genome-build source buildName */
{
if (g3f->genomeBuildSource != NULL)
fprintf(fh, "##genome-build %s %s\n", g3f->genomeBuildSource, g3f->genomeBuildName);
}
static void parseMeta(struct gff3File *g3f, char *line)
/* parse a meta line of a gff3 file */
{
eraseTrailingSpaces(line);
if (sameString("###", line))
; // ignore
else if (sameString("##FASTA", line))
parseFasta(g3f);
else if (startsWithWord("##sequence-region", line))
parseSequenceRegion(g3f, line);
else if (startsWithWord("##feature-ontology", line))
parseFeatureOntology(g3f, line);
else if (startsWithWord("##attribute-ontology", line))
parseAttributeOntology(g3f, line);
else if (startsWithWord("##source-ontology", line))
parseSourceOntology(g3f, line);
else if (startsWithWord("##species", line))
parseSpecies(g3f, line);
else if (startsWithWord("##genome-build", line))
parseGenomeBuild(g3f, line);
else
gff3FileErr(g3f, "invalid meta line: %s", line);
}
static void parseLine(struct gff3File *g3f, char *line)
/* parse one line of a gff3 file */
{
if (startsWith("##", line))
parseMeta(g3f, line);
else if (!startsWith("#", line) && (strlen(line) > 0))
parseAnn(g3f, line);
}
static void parseHeader(struct gff3File *g3f)
/* parse and validate a GFF3 header */
{
char *line;
if (!lineFileNext(g3f->lf, &line, NULL))
gff3FileErr(g3f, "empty GFF file, must have header");
char *ver = skipToSpaces(line);
if (*ver != '\0')
{
*ver++ = '\0';
ver = trimSpaces(ver);
}
if (!(sameString(line, "##gff-version") && sameString(ver, "3")))
gff3FileErr(g3f, "invalid GFF3 header");
}
static void parseFile(struct gff3File *g3f)
/* do parsing phase of reading a GFF3 file */
{
g3f->lf = lineFileOpen(g3f->fileName, TRUE);
parseHeader(g3f);
char *line;
while (lineFileNext(g3f->lf, &line, NULL))
parseLine(g3f, line);
lineFileClose(&g3f->lf);
slReverse(&g3f->anns);
}
static struct gff3Ann *resolveRef(struct gff3Ann *g3a, char *id, char *attr)
/* resolve a link for an attribute */
{
struct gff3Ann *ann = gff3FileFindAnn(g3a->file, id);
if (ann == NULL)
gff3AnnErr(g3a, "Can't find annotation record \"%s\" referenced by \"%s\" %s attribute", id, g3a->id, attr);
return ann;
}
static struct gff3AnnRef *resolveRefs(struct gff3Ann *g3a, struct slName *ids, char *attr)
/* resolve links for an attribute */
{
struct gff3AnnRef *refs = NULL;
struct slName *id;
for (id = ids; id != NULL; id = id->next)
{
struct gff3Ann *ann = resolveRef(g3a, id->name, attr);
if (ann != NULL)
slSafeAddHead(&refs, gff3AnnRefAlloc(ann));
}
return refs;
}
static void resolveAnn(struct gff3Ann *g3a)
/* resolve links for an gff3Ann */
{
g3a->parents = resolveRefs(g3a, g3a->parentIds, gff3AttrParent);
if (g3a->parents == NULL)
slSafeAddHead(&g3a->file->roots, gff3AnnRefAlloc(g3a));
else
{
struct gff3AnnRef *par;
for (par = g3a->parents; par != NULL; par = par->next)
slSafeAddHead(&par->ann->children, gff3AnnRefAlloc(g3a));
}
if (g3a->derivesFromId != NULL)
g3a->derivesFrom = resolveRef(g3a, g3a->derivesFromId, gff3AttrDerivesFrom);
}
static void resolveFile(struct gff3File *g3f)
/* do resolution phase of reading a GFF3 file */
{
struct gff3Ann *g3a;
for (g3a = g3f->anns; g3a != NULL; g3a = g3a->next)
resolveAnn(g3a);
// reorder just for test reproducibility
slReverse(&g3f->seqRegions);
slReverse(&g3f->featureOntologies);
slReverse(&g3f->attributeOntologies);
slReverse(&g3f->sourceOntologies);
slReverse(&g3f->species);
slReverse(&g3f->seqs);
}
static struct gff3File *gff3FileNew()
/* construct a new, empty gff3File object */
{
struct gff3File *g3f;
AllocVar(g3f);
g3f->byId = hashNew(0);
g3f->pool = hashNew(0);
return g3f;
}
struct gff3File *gff3FileOpen(char *fileName, int maxErr, FILE *errFh)
/* Parse a GFF3 file into a gff3File object. If maxErr not zero, then
* continue to parse until this number of error have been reached. A maxErr
* less than zero does not stop reports all errors. Write errors to errFh,
* if NULL, use stderr. */
{
struct gff3File *g3f = gff3FileNew();
g3f->fileName = gff3FileCloneStr(g3f, fileName);
g3f->errFh = (errFh != NULL) ? errFh : stderr;
-g3f->maxErr = (maxErr < 0) ? MAXINT : maxErr;
+g3f->maxErr = (maxErr < 0) ? INT_MAX : maxErr;
parseFile(g3f);
resolveFile(g3f);
if (g3f->errCnt > 0)
errAbort("GFF3: %d parser errors", g3f->errCnt);
return g3f;
}
void gff3FileFree(struct gff3File **g3fPtr)
/* Free a gff3File object */
{
struct gff3File *g3f = *g3fPtr;
if (g3f != NULL)
{
hashFree(&g3f->byId);
hashFree(&g3f->pool);
hashFree(&g3f->seqRegionMap);
freeMem(g3f);
*g3fPtr = NULL;
}
}
struct gff3Ann *gff3FileFindAnn(struct gff3File *g3f, char *id)
/* find an annotation record by id, or NULL if not found. */
{
return hashFindVal(g3f->byId, id);
}
static void writeMeta(struct gff3File *g3f, FILE *fh)
/* write meta data */
{
fputs("##gff-version 3\n", fh);
writeSequenceRegions(g3f, fh);
writeFeatureOntologies(g3f, fh);
writeAttributeOntologies(g3f, fh);
writeSourceOntologies(g3f, fh);
writeSpecies(g3f, fh);
writeGenomeBuild(g3f, fh);
}
void gff3FileWrite(struct gff3File *g3f, char *fileName)
/* write contents of an GFF3File object to a file */
{
FILE *fh = mustOpen(fileName, "w");
writeMeta(g3f, fh);
struct gff3Ann *g3a;
for (g3a = g3f->anns; g3a != NULL; g3a = g3a->next)
writeAnn(g3a, fh);
writeFastas(g3f, fh);
carefulClose(&fh);
}