Exemplo n.º 1
0
void faToTwoBit(char *inFiles[], int inFileCount, char *outFile)
/* Convert inFiles in fasta format to outfile in 2 bit 
 * format. */
{
struct twoBit *twoBitList = NULL, *twoBit;
int i;
struct hash *uniqHash = newHash(18);
FILE *f;

for (i=0; i<inFileCount; ++i)
    {
    char *fileName = inFiles[i];
    struct lineFile *lf = lineFileOpen(fileName, TRUE);
    struct dnaSeq seq;
    ZeroVar(&seq);
    while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
        {
	if (seq.size == 0)
	    {
	    warn("Skipping item %s which has no sequence.\n",seq.name);
	    continue;
	    }
	    
        /* strip off version number */
        if (stripVersion)
            {
            char *sp = NULL;
            sp = strchr(seq.name,'.');
            if (sp != NULL)
                *sp = '\0';
            }

        if (hashLookup(uniqHash, seq.name))
            {
            if (!ignoreDups)
                errAbort("Duplicate sequence name %s", seq.name);
            else
                continue;
            }
	hashAdd(uniqHash, seq.name, NULL);
	if (noMask)
	    faToDna(seq.dna, seq.size);
	else
	    unknownToN(seq.dna, seq.size);
	twoBit = twoBitFromDnaSeq(&seq, !noMask);
	slAddHead(&twoBitList, twoBit);
	}
    lineFileClose(&lf);
    }
slReverse(&twoBitList);
f = mustOpen(outFile, "wb");
twoBitWriteHeader(twoBitList, f);
for (twoBit = twoBitList; twoBit != NULL; twoBit = twoBit->next)
    {
    twoBitWriteOne(twoBit, f);
    }
carefulClose(&f);
}
Exemplo n.º 2
0
void twoBitMask(char *inName, char *maskName, char *outName)
/* twoBitMask - apply masking to a .2bit file, creating a new .2bit file. */
{
    struct hash *tbHash = hashNew(20);
    struct hash *bitmapHash = hashNew(20);
    struct twoBit *twoBitList = NULL;
    struct twoBit *twoBit = NULL;
    FILE *f = NULL;

    if (! twoBitIsFile(inName))
    {
        if (twoBitIsSpec(inName))
            errAbort("Sorry, this works only on whole .2bit files, not specs.");
        else
            errAbort("Input %s does not look like a proper .2bit file.", inName);
    }

    twoBitList = slurpInput(inName, tbHash, bitmapHash);

    /* Read mask data into bitmapHash, store it in twoBits: */
    if ((type && endsWith(type, "bed")) || endsWith(maskName, ".bed"))
        maskWithBed(maskName, tbHash, bitmapHash);
    else if ((type && endsWith(type, "out")) || endsWith(maskName, ".out"))
        maskWithOut(maskName, tbHash, bitmapHash);
    else
        errAbort("Sorry, maskFile must end in \".bed\" or \".out\".");

    /* Create a new .2bit file, write it out from twoBits. */
    f = mustOpen(outName, "wb");
    twoBitWriteHeader(twoBitList, f);
    for (twoBit = twoBitList; twoBit != NULL; twoBit = twoBit->next)
    {
        twoBitWriteOne(twoBit, f);
    }
    carefulClose(&f);

    /* Don't bother freeing twoBitList and hashes here -- just exit. */
}