void copyPslXaToTab(char *pslFile, char *tabFile)
/* copy a single PSL XA to the tab file */
{
struct xAli *xa;
char *row[23];
struct lineFile *lf = lineFileOpen(pslFile, TRUE);
struct pipeline *pl = NULL;
FILE *tabFh = NULL;
if (noSort)
tabFh = mustOpen(tabFile, "w");
else
{
if (pslCreateOpts & PSL_WITH_BIN)
pl = pipelineOpen(outPipeBin, pipelineWrite, tabFile, NULL);
else
pl = pipelineOpen(outPipeNoBin, pipelineWrite, tabFile, NULL);
tabFh = pipelineFile(pl);
}
while (lineFileRow(lf, row))
{
xa = xAliLoad(row);
if (pslCreateOpts & PSL_WITH_BIN)
fprintf(tabFh, "%u\t", hFindBin(xa->tStart, xa->tEnd));
xAliTabOut(xa, tabFh);
xAliFree(&xa);
}
lineFileClose(&lf);
if (noSort)
carefulClose(&tabFh);
else
{
pipelineWait(pl);
pipelineFree(&pl);
}
}
void copyPslToTab(char *pslFile, char *tabFile)
/* copy a single PSL to the tab file */
{
struct psl *psl;
struct lineFile *lf = pslFileOpen(pslFile);
struct pipeline *pl = NULL;
FILE *tabFh = NULL;
if (noSort)
tabFh = mustOpen(tabFile, "w");
else
{
if (pslCreateOpts & PSL_WITH_BIN)
pl = pipelineOpen(outPipeBin, pipelineWrite, tabFile, NULL);
else
pl = pipelineOpen(outPipeNoBin, pipelineWrite, tabFile, NULL);
tabFh = pipelineFile(pl);
}
while ((psl = pslNext(lf)) != NULL)
{
if (pslCreateOpts & PSL_WITH_BIN)
fprintf(tabFh, "%u\t", hFindBin(psl->tStart, psl->tEnd));
pslTabOut(psl, tabFh);
pslFree(&psl);
}
lineFileClose(&lf);
if (noSort)
carefulClose(&tabFh);
else
{
pipelineWait(pl);
pipelineFree(&pl);
}
}
struct pipeline *pipelineOpen1(char **cmd, unsigned opts,
char *otherEndFile, char *stderrFile)
/* like pipelineOpen(), only takes a single command */
{
char **cmds[2];
cmds[0] = cmd;
cmds[1] = NULL;
return pipelineOpen(cmds, opts, otherEndFile, stderrFile);
}
static void runCommandAppend(char *cmd[], char *program, char *inFile, char *outFile)
/* Use the pipeline module to run a single command pipelineWrite|pipelineAppend. */
{
char **cmds[2];
cmds[0] = cmd;
cmds[1] = NULL;
cmd[0] = program;
cmd[1] = inFile;
struct pipeline *pl = pipelineOpen(cmds, pipelineWrite|pipelineAppend, outFile, NULL);
pipelineClose(&pl);
}
static struct pipeline *openPslSortPipe(char *pslFile)
/* open pipeline that sorts psl */
{
static char *zcatCmd[] = {"zcat", NULL};
static char *bzcatCmd[] = {"zcat", NULL};
static char *sortCmd[] = {"sort", "-k", "14,14", "-k", "16,16n", "-k", "17,17nr", NULL};
int iCmd = 0;
char **cmds[3];
if (endsWith(pslFile, ".gz") || endsWith(pslFile, ".Z"))
cmds[iCmd++] = zcatCmd;
else if (endsWith(pslFile, ".bz2"))
cmds[iCmd++] = bzcatCmd;
cmds[iCmd++] = sortCmd;
cmds[iCmd++] = NULL;
return pipelineOpen(cmds, pipelineRead, pslFile, NULL);
}
static void generateImgFiles(struct hgdpGeo *geo, char finalEpsFile[PATH_LEN],
char finalPdfFile[PATH_LEN], char finalPngFile[PATH_LEN])
/* Using the frequencies given in geo and the population latitude and longitude
* given above, plot allele frequency pie charts for each population on a world map.
* Work in a temporary trash dir and then move result files to the given paths. */
{
// The Generic Mapping Tools commands must have a writeable ./ and $HOME.
// Use trashDirFile as a directory name, cd to that and work there.
char cwd[PATH_LEN];
if (getcwd(cwd, sizeof(cwd)) == NULL)
errAbort("PATH_LEN (%d) is too short.", PATH_LEN);
struct tempName dirTn;
trashDirFile(&dirTn, "hgc", "hgdpGeo", "");
makeDirs(dirTn.forCgi);
mustChdir(dirTn.forCgi);
char *realHome = getenv("HOME");
setenv("HOME", ".", TRUE);
// Make trash files with coordinate specs for pie charts and full circles:
char rootName[FILENAME_LEN];
splitPath(dirTn.forCgi, NULL, rootName, NULL);
char pieFile[FILENAME_LEN], circleFile[FILENAME_LEN];
safef(pieFile, sizeof(pieFile), "%s_pie.txt", rootName);
safef(circleFile, sizeof(circleFile), "%s_circle.txt", rootName);
FILE *fPie = mustOpen(pieFile, "w");
FILE *fCir = mustOpen(circleFile, "w");
int i;
for (i = 0; i < HGDPGEO_POP_COUNT; i++)
{
FILE *f = (geo->popFreqs[i] == 1.0) ? fCir : fPie;
fprintf(f, "%.4f %.4f 0.65 0 %.4f\n",
pops[i].latitude, pops[i].longitude, geo->popFreqs[i]*360);
}
fclose(fPie);
fclose(fCir);
// Build up an EPS image: copy a baseline EPS (map background), add SNP and allele labels,
// and use ps2xy commands to allele frequency pie charts.
char epsFile[FILENAME_LEN];
safef(epsFile, sizeof(epsFile), "%s.eps", rootName);
char mapBgEps[PATH_LEN];
safef(mapBgEps, sizeof(mapBgEps), "%s/hgcData/hgdpGeoMap.eps", cwd);
copyFile(mapBgEps, epsFile);
FILE *fEps = mustOpen(epsFile, "a");
fprintf(fEps, hgdpGeoLabelFormat, geo->name, geo->name,
geo->ancestralAllele, geo->ancestralAllele, geo->derivedAllele, geo->derivedAllele);
fclose(fEps);
//- run psxy on circle/pie spec trash files for AfrEurAsia and America
char *psxy = cfgOption("hgc.psxyPath");
if (isEmpty(psxy))
errAbort("How did this get called? hg.conf doesn't have hgc.psxyPath.");
runCommandAppend(psxyOrangeAeaCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyPieAeaCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyBlueAeaCmd, psxy, circleFile, epsFile);
runCommandAppend(psxyOrangeAmCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyPieAmCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyBlueAmCmd, psxy, circleFile, epsFile);
// Make PDF and PNG:
struct pipeline *pl;
char pdfFile[FILENAME_LEN], pngFile[FILENAME_LEN];
safef(pdfFile, sizeof(pdfFile), "%s.pdf", rootName);
safef(pngFile, sizeof(pngFile), "%s.png", rootName);
char *ps2pdfCmd[] = {"ps2pdf", epsFile, pdfFile, NULL};
char **cmdsPdf[] = {ps2pdfCmd, NULL};
pl = pipelineOpen(cmdsPdf, pipelineWrite, "/dev/null", NULL);
pipelineClose(&pl);
char *ps2raster = cfgOption("hgc.ps2rasterPath");
char *ghostscript = cfgOption("hgc.ghostscriptPath");
char gsOpt[PATH_LEN];
safef(gsOpt, sizeof(gsOpt), "-G%s", ghostscript);
char *ps2RasterPngCmd[] = {ps2raster, gsOpt, "-P", "-A", "-Tg", "-E150", epsFile, NULL};
char **cmdsPng[] = {ps2RasterPngCmd, NULL};
pl = pipelineOpen(cmdsPng, pipelineRead, "/dev/null", NULL);
pipelineClose(&pl);
// Back to our usual working directory and $HOME:
if (realHome == NULL)
unsetenv("HOME");
else
setenv("HOME", realHome, TRUE);
mustChdir(cwd);
// Move the result files into place:
char tmpPath[PATH_LEN];
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, epsFile);
mustRename(tmpPath, finalEpsFile);
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, pdfFile);
mustRename(tmpPath, finalPdfFile);
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, pngFile);
mustRename(tmpPath, finalPngFile);
// Clean up the temporary working directory (trash cleaner script doesn't
// remove empty dirs:
removeDir(dirTn.forCgi);
}
