FILE* gbMustOpenOutput(char* path)
/* Open an output file for atomic file creation. Create the directory if it
* doesn't exist. If the path has one of the compress extensions (.gz, .Z,
* .bz2) the output is compressed. File is opened under a tmp name until
* installed. */
{
char tmpPath[PATH_LEN];
gbGetOutputTmp(path, tmpPath);
gbMakeFileDirs(tmpPath);
return gzMustOpen(tmpPath, "w");
}
FILE *openSortOutput(char *fileName, char **sortSpec)
/* Open a pipeline to sort and compress output. SortSpec is null-terminated
* list of fields options to pass to sort. gSortTmpDir maybe null.
* gbOutputRename is used to install and close.
*/
{
struct gbPipeline *pipeline;
char tmpPath[PATH_LEN];
char **compressor;
char **sortCmd, **cmds[3];
int nSort, iSort = 0, i;
/* sort cmd, nSort includes cmd and NULL */
for (nSort = 0; sortSpec[nSort] != NULL; nSort++)
continue;
if (gSortTmp != NULL)
nSort += 2;
nSort += 2; /* for "sort" and NULL */
sortCmd = alloca(nSort*sizeof(char*));
sortCmd[iSort++] = "sort";
if (gSortTmp != NULL)
{
sortCmd[iSort++] = "-T";
sortCmd[iSort++] = gSortTmp;
}
for (i = 0; sortSpec[i] != NULL; i++)
sortCmd[iSort++] = sortSpec[i];
sortCmd[iSort] = NULL;
assert(iSort < nSort);
cmds[0] = sortCmd;
cmds[1] = NULL;
/* compress process, if needed */
compressor = gbGetCompressor(fileName, "w");
if (compressor != NULL)
{
cmds[1] = compressor;
cmds[2] = NULL;
}
/* tmp name to output to */
gbGetOutputTmp(fileName, tmpPath);
gbMakeFileDirs(tmpPath);
pipeline = gbPipelineCreate(cmds, PIPELINE_WRITE|PIPELINE_FDOPEN, NULL,
tmpPath);
return gbPipelineFile(pipeline);
}
void getTestSubset(int numMrnas, int numEsts, char *accList,
char* selectAccFile, char* relName, char* database,
char* outDir)
/* Get the test subset. */
{
struct gbRelease* release;
struct hash* accTbl = hashNew(20);
unsigned types = 0;
/* note, we find mRNAs and ESTs seperately, but extract in one pass, as
* daily updates have both in a single file */
if (numMrnas > 0)
types |= GB_MRNA;
if (numEsts > 0)
types |= GB_EST;
release = loadIndex(relName, types, database);
if (selectAccFile != NULL)
getRequestedAccs(selectAccFile, release, accTbl);
if (numMrnas > 0)
findAccs(numMrnas, GB_MRNA, release, accTbl);
if (numEsts > 0)
findAccs(numEsts, GB_EST, release, accTbl);
copyAccs(release, types, accTbl, outDir);
if (accList != NULL)
{
FILE *accListFh;
struct hashCookie cookie;
struct hashEl* hel;
gbMakeFileDirs(accList);
accListFh = mustOpen(accList, "w");
cookie = hashFirst(accTbl);
while ((hel = hashNext(&cookie)) != NULL)
fprintf(accListFh, "%s\n", hel->name);
carefulClose(&accListFh);
}
hashFree(&accTbl);
gbIndexFree(&release->index);
}
