void txOrtho(char *inAgx, char *inChain, char *inNet, char *orthoAgx, char *outEdges)
/* txOrtho - Produce list of shared edges between two transcription graphs in two species. */
{
/* Load up input and create output file */
struct txGraph *inGraphList = txGraphLoadAll(inAgx);
verbose(1, "Loaded %d input graphs in %s\n", slCount(inGraphList), inAgx);
struct hash *chainHash = allChainsHash(inChain);
verbose(1, "Read %d chains from %s\n", chainHash->elCount, inChain);
struct hash *netHash = netToBkHash(inNet);
verbose(1, "Read %d nets from %s\n", netHash->elCount, inNet);
struct txGraph *orthoGraphList = txGraphLoadAll(orthoAgx);
verbose(1, "Loaded %d ortho graphs in %s\n", slCount(orthoGraphList), orthoAgx);
struct hash *orthoGraphHash = txgIntoKeeperHash(orthoGraphList);
verbose(1, "%d ortho chromosomes/scaffolds\n", orthoGraphHash->elCount);
FILE *f = mustOpen(outEdges, "w");
/* Loop through inGraphList. */
struct txGraph *inGraph;
for (inGraph = inGraphList; inGraph != NULL; inGraph = inGraph->next)
{
verbose(2, "Processing %s %s:%d-%d strand %s\n",
inGraph->name, inGraph->tName, inGraph->tStart, inGraph->tEnd,
inGraph->strand);
writeOrthoEdges(inGraph, chainHash, netHash, orthoGraphHash, f);
}
carefulClose(&f);
}
struct chain *chainFromId(int id)
/** Return a chain given the id. */
{
static struct hash *chainHash = NULL;
char key[128];
struct chain *chain = NULL;
if(id == 0)
return NULL;
if(chainHash == NULL)
{
char *chainFile = optionVal("chainFile", NULL);
if(chainFile == NULL)
errAbort("orthoSplice::chainFromId() - Can't find file for 'chainFile' parameter");
chainHash = allChainsHash(chainFile);
}
safef(key, sizeof(key), "%d", id);
chain = hashFindVal(chainHash, key);
if(chain == NULL && id != 0)
warn("Chain not found for id: %d", id);
return chain;
}
