void parseSeqs(string filename, SeqSet &data) {
ifstream input;
SeqStream input_stream(openSeqFile(filename, input));
if(!input_stream.good()) {
throw("File stream is in a bad state");
}
string format = guessFormat(input_stream);
if(format == "fasta") {
try {
parseFasta(input_stream, filename, data);
} catch(...) {
input.close();
throw;
}
} else if(format == "fastq") {
try {
parseFastq(input_stream, filename, data);
} catch(...) {
input.close();
throw;
}
} else {
input.close();
throw("Unrecognized format");
}
input.close();
}
void parseAli(char *orderFileName, char *fastaFile,
alignFunc afunc, columnFunc cfunc, void *closure)
/* Parse a file of alignments. */
{
struct hash *seqHash = newHash(5);
struct slName *list = getOrderList(orderFileName);
int numSpecies = fillSeqHash(list, seqHash);
struct lineFile *lf = lineFileOpen(fastaFile, TRUE);
parseFasta(lf, numSpecies, list, seqHash, afunc, cfunc, closure);
slNameFreeList(&list);
}
static struct traceInfo* readFastaFiles(int numFiles, char **fastaFiles)
/* read data for all fasta files */
{
int i;
struct traceInfo* traceInfoList = NULL;
for (i = 0; i < numFiles; i++)
{
parseFasta(fastaFiles[i], &traceInfoList);
}
return traceInfoList;
}
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);
}
