void fakeFinContigs(char *agpName, char *faName, char *finDir, char *rootName, char *finFaDir, char *ooVer)
/* fakeFinContigs - Fake up contigs for a finished chromosome. */
{
struct contig *contigList = NULL, *contig = NULL;
struct agpFrag *agp;
struct lineFile *lf = lineFileOpen(agpName, TRUE);
char *line, *words[16];
int lineSize, wordCount;
int contigIx = 0;
char liftDir[512], contigDir[512], path[512];
char chrom[128];
FILE *f;
struct dnaSeq *seq;
int fragIx;
/* Build up contig list by scanning agp file. */
printf("Reading %s\n", lf->fileName);
while (lineFileNext(lf, &line, &lineSize))
{
if (line[0] == '#' || line[0] == 0)
continue;
wordCount = chopLine(line, words);
if (wordCount < 5)
errAbort("Expecting at least 5 words line %d of %s", lf->lineIx, lf->fileName);
if (words[4][0] == 'N' || words[4][0] == 'U')
{
contig = NULL;
continue;
}
lineFileExpectWords(lf, 9, wordCount);
agp = agpFragLoad(words);
// file is 1-based but agpFragLoad() now assumes 0-based:
agp->chromStart -= 1;
agp->fragStart -= 1;
if (contig == NULL)
{
AllocVar(contig);
sprintf(contig->name, "%s%d", rootName, ++contigIx);
contig->startOffset = agp->chromStart;
slAddHead(&contigList, contig);
}
else
{
if (contig->agpList != NULL && contig->agpList->chromEnd != agp->chromStart)
errAbort("Start doesn't match previous end line %d of %s",
lf->lineIx, lf->fileName);
}
if (agp->chromEnd - agp->chromStart != agp->fragEnd - agp->fragStart)
errAbort("Chrom and frag size mismatch line %d of %s", lf->lineIx, lf->fileName);
slAddHead(&contig->agpList, agp);
contig->endOffset = agp->chromEnd;
}
slReverse(&contigList);
for (contig = contigList; contig != NULL; contig = contig->next)
slReverse(&contig->agpList);
lineFileClose(&lf);
/* Load up chromosome sequence and make sure it is in one piece. */
printf("Reading %s\n", faName);
seq = faReadAllDna(faName);
if (slCount(seq) != 1)
errAbort("Got %d sequences in %s, can only handle one.", slCount(seq), faName);
/* Fix up agp coordinates. Make a directory for each contig. Fill it with
* .fa .agp barge.NN files for that contig. */
printf("Writing contig dirs\n");
for (contig = contigList; contig != NULL; contig = contig->next)
{
/* Make Contig dir. */
sprintf(contigDir, "%s/%s", finDir, contig->name);
makeDir(contigDir);
/* Make contig.agp file. */
sprintf(path, "%s/%s.agp", contigDir, contig->name);
f = mustOpen(path, "w");
fragIx = 0;
for (agp = contig->agpList; agp != NULL; agp = agp->next)
{
char buf[128];
sprintf(buf, "%s/%s", skipChr(agp->chrom), contig->name);
freez(&agp->chrom);
agp->chrom = cloneString(buf);
agp->chromStart -= contig->startOffset;
agp->chromEnd -= contig->startOffset;
agp->ix = ++fragIx;
agpFragTabOut(agp, f);
}
carefulClose(&f);
/* Make ooGreedy.NN.gl file */
sprintf(path, "%s/%s.%s.gl", contigDir, "ooGreedy", ooVer);
f = mustOpen(path, "w");
for (agp = contig->agpList; agp != NULL; agp = agp->next)
{
if (agp->type[0] != 'N' && agp->type[0] != 'U')
{
fprintf(f, "%s_1\t%d\t%d\t%s\n", agp->frag,
agp->chromStart,
agp->chromEnd,
agp->strand);
}
}
carefulClose(&f);
/* Make contig.fa file. */
sprintf(path, "%s/%s.fa", contigDir, contig->name);
faWrite(path, contig->name, seq->dna + contig->startOffset,
contig->endOffset - contig->startOffset);
/* Make contig/barge file. */
sprintf(path, "%s/barge.%s", contigDir, ooVer);
f = mustOpen(path, "w");
fprintf(f, "Barge (Connected Clone) File ooGreedy Version %s\n", ooVer);
fprintf(f, "\n");
fprintf(f, "start accession size overlap maxClone maxOverlap\n");
fprintf(f, "------------------------------------------------------------\n");
for (agp = contig->agpList; agp != NULL; agp = agp->next)
{
char clone[128];
strcpy(clone, agp->frag);
chopSuffix(clone);
fprintf(f, "%d\t%s\t%d\t100\tn/a\t0\n", agp->chromStart,
clone, agp->chromEnd);
}
carefulClose(&f);
/* Make contig/gold file. */
sprintf(path, "%s/gold.%s", contigDir, ooVer);
f = mustOpen(path, "w");
fragIx = 0;
for (agp = contig->agpList; agp != NULL; agp = agp->next)
{
char fragName[128];
struct agpFrag frag = *agp;
sprintf(fragName, "%s_1", agp->frag);
frag.frag = fragName;
frag.type[0] = '0';
agpFragTabOut(&frag, f);
}
carefulClose(&f);
}
/* Create lift subdirectory. */
printf("Creating lift files\n");
sprintf(liftDir, "%s/lift", finDir);
makeDir(liftDir);
/* Create lift/oOut.lst file (just a list of contigs). */
sprintf(path, "%s/oOut.lst", liftDir);
f = mustOpen(path, "w");
for (contig = contigList; contig != NULL; contig = contig->next)
fprintf(f, "%s/%s.fa.out\n", contig->name, contig->name);
carefulClose(&f);
/* Create lift/ordered.lst file (just a list of contigs). */
sprintf(path, "%s/ordered.lst", liftDir);
f = mustOpen(path, "w");
for (contig = contigList; contig != NULL; contig = contig->next)
fprintf(f, "%s\n", contig->name);
carefulClose(&f);
/* Create lift/ordered.lft file. */
sprintf(path, "%s/ordered.lft", liftDir);
f = mustOpen(path, "w");
splitPath(faName, NULL, chrom, NULL);
for (contig = contigList; contig != NULL; contig = contig->next)
fprintf(f, "%d\t%s/%s\t%d\t%s\t%d\n",
contig->startOffset, skipChr(chrom), contig->name,
contig->endOffset - contig->startOffset,
chrom, seq->size);
carefulClose(&f);
}
void splitAgp(char *agpName, char *goldFileName, char *gapFileName)
/* Split up agp file into gold and gap files. */
{
struct lineFile *lf;
char *words[16];
int wordCount;
FILE *goldTab, *gapTab;
/* Scan through .agp file splitting it into gold
* and gap components. */
goldTab = mustOpen(goldFileName, "w");
gapTab = mustOpen(gapFileName, "w");
lf = lineFileOpen(agpName, TRUE);
while ((wordCount = lineFileChop(lf, words)) > 0)
{
int start, end;
if (wordCount < 5)
errAbort("Short line %d of %s", lf->lineIx, lf->fileName);
int len = strlen(words[0]);
if (len > maxChromNameSize)
{
maxChromNameSize = len;
if (maxChromNameSize > 254)
errAbort("ERROR: chrom name size is over 254(%d) characters: "
"'%s'", maxChromNameSize, words[0]);
}
start = sqlUnsigned(words[1])-1;
end = sqlUnsigned(words[2]);
if (words[4][0] == 'N' || words[4][0] == 'U')
{
struct agpGap gap;
agpGapStaticLoad(words, &gap);
gap.chromStart -= 1;
fprintf(gapTab, "%u\t", hFindBin(start, end));
agpGapTabOut(&gap, gapTab);
verbose(3,"#GAP\t%s:%d-%d\n", gap.chrom, gap.chromStart, gap.chromEnd);
}
else
{
struct agpFrag gold;
agpFragStaticLoad(words, &gold);
agpFragValidate(&gold);
len = strlen(words[5]);
if (len > maxFragNameSize)
{
maxFragNameSize = len;
if (maxFragNameSize > 254)
errAbort("ERROR: fragment name size is over 254(%d) "
"characters: '%s'", maxFragNameSize, words[5]);
}
// file is 1-based. agpFragLoad() now assumes 0-based.
// and agpFragTabOut() will assume 1-based, but we will load
// the generated file straight into the database, so
// subtract 2:
gold.chromStart -= 2;
gold.fragStart -= 2;
fprintf(goldTab, "%u\t", hFindBin(start, end));
agpFragTabOut(&gold, goldTab);
}
}
lineFileClose(&lf);
carefulClose(&goldTab);
carefulClose(&gapTab);
}