void liftOver(char *oldFile, char *mapFile, double minMatch,
double minBlocks, int minSizeT, int minSizeQ,
int minChainT, int minChainQ, bool multiple, bool noSerial, char *chainTable,
char *newFile, char *unmappedFile)
/* liftOver - Move annotations from one assembly to another. */
{
struct hash *chainHash = newHash(0); /* Old chromosome name keyed, chromMap valued. */
FILE *mapped = mustOpen(newFile, "w");
FILE *unmapped = mustOpen(unmappedFile, "w");
int errCt;
if (!fileExists(oldFile))
errAbort("Can't find file: %s\n", oldFile);
verbose(1, "Reading liftover chains\n");
readLiftOverMap(mapFile, chainHash);
verbose(1, "Mapping coordinates\n");
if (optionExists("gff"))
{
fprintf(stderr, "WARNING: -gff is not recommended.\nUse 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'\n");
if (multiple)
errAbort("ERROR: -multiple is not supported for -gff.");
if (chainTable)
errAbort("ERROR: -chainTable is not supported for -gff.");
liftOverGff(oldFile, chainHash, minMatch, minBlocks, mapped, unmapped);
}
else if (optionExists("genePred"))
{
if (chainTable)
errAbort("ERROR: -chainTable is not supported for -genePred.");
liftOverGenePred(oldFile, chainHash, minMatch, minBlocks, fudgeThick,
mapped, unmapped, multiple);
}
else if (optionExists("sample"))
{
if (multiple)
errAbort("ERROR: -multiple is not supported for -sample.");
if (chainTable)
errAbort("ERROR: -chainTable is not supported for -sample.");
liftOverSample(oldFile, chainHash, minMatch, minBlocks, fudgeThick,
mapped, unmapped);
}
else if (optionExists("pslT"))
{
verbose(1, "Consider using pslMap instead of liftOver for PSL.\n");
if (multiple)
errAbort("ERROR: -multiple is not supported for -pslT.");
if (chainTable)
errAbort("ERROR: -chainTable is not supported for -pslT.");
liftOverPsl(oldFile, chainHash, minMatch, minBlocks, fudgeThick,
mapped, unmapped);
}
else if (optionExists("ends"))
liftOverBedPlusEnds(oldFile, chainHash, minMatch, minBlocks,
minSizeT, minSizeQ,
minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial,
chainTable, bedPlus, hasBin, tabSep, ends, &errCt);
else if (optionExists("bedPlus"))
liftOverBedPlus(oldFile, chainHash, minMatch, minBlocks,
minSizeT, minSizeQ,
minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial,
chainTable, bedPlus, hasBin, tabSep, &errCt);
else if (optionExists("positions"))
liftOverPositions(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ,
minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple,
chainTable, &errCt);
else
liftOverBed(oldFile, chainHash, minMatch, minBlocks, minSizeT, minSizeQ,
minChainT, minChainQ, fudgeThick, mapped, unmapped, multiple, noSerial,
chainTable, &errCt);
if (!optionExists("positions"))
/* I guess liftOverPositions closes these files. This is a little akward though. */
{
carefulClose(&mapped);
carefulClose(&unmapped);
}
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
/* struct liftOverChain *chainList = NULL, *chain; */
char *userData;
/* char *dataFile; */
char *dataFormat;
char *organism;
char *db;
float minBlocks, minMatch;
boolean multiple, fudgeThick;
int minSizeQ, minSizeT;
boolean refreshOnly = FALSE;
/* char *err = NULL; */
struct liftOverChain *chainList = NULL, *choice;
cart = theCart;
if (cgiOptionalString(HGLFT_ERRORHELP_VAR))
{
puts("<PRE>");
puts(liftOverErrHelp());
//system("/usr/bin/cal");
puts("</PRE>");
return;
}
/* Get data to convert - from userData variable, or if
* that is empty from a file. */
if (cartOptionalString(cart, "SubmitFile"))
userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
else
userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
dataFormat = cartCgiUsualString(cart, HGLFT_DATAFORMAT_VAR, DEFAULT_FORMAT);
cartWebStart(cart, NULL, "Lift Genome Annotations");
getDbAndGenome(cart, &db, &organism, oldVars);
chainList = liftOverChainListFiltered();
choice = defaultChoices(chainList, db);
if (choice == NULL)
errAbort("Sorry, no conversions available from this assembly\n");
minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
minSizeT = cartCgiUsualInt(cart, HGLFT_MINSIZET, choice->minSizeT);
minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);
fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE);
multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE);
refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0);
webMain(choice, dataFormat, multiple);
liftOverChainFreeList(&chainList);
if (!refreshOnly && userData != NULL && userData[0] != '\0')
{
struct hash *chainHash = newHash(0);
char *chainFile;
struct tempName oldTn, mappedTn, unmappedTn;
FILE *old, *mapped, *unmapped;
char *line;
int lineSize;
char *fromDb, *toDb;
int ct = 0, errCt = 0;
/* read in user data and save to file */
makeTempName(&oldTn, HGLFT, ".user");
old = mustOpen(oldTn.forCgi, "w");
fputs(userData, old);
fputs("\n", old); /* in case user doesn't end last line */
carefulClose(&old);
chmod(oldTn.forCgi, 0666);
/* setup output files -- one for converted lines, the other
* for lines that could not be mapped */
makeTempName(&mappedTn, HGLFT, ".bed");
makeTempName(&unmappedTn, HGLFT, ".err");
mapped = mustOpen(mappedTn.forCgi, "w");
chmod(mappedTn.forCgi, 0666);
unmapped = mustOpen(unmappedTn.forCgi, "w");
chmod(unmappedTn.forCgi, 0666);
fromDb = cgiString(HGLFT_FROMDB_VAR);
toDb = cgiString(HGLFT_TODB_VAR);
chainFile = liftOverChainFile(fromDb, toDb);
if (chainFile == NULL)
errAbort("ERROR: Can't convert from %s to %s: no chain file loaded",
fromDb, toDb);
readLiftOverMap(chainFile, chainHash);
if (sameString(dataFormat, WIGGLE_FORMAT))
/* TODO: implement Wiggle */
{}
else if (sameString(dataFormat, POSITION_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
/* ignore multiple, it must be false when position is used */
ct = liftOverPositions(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, FALSE, NULL, &errCt);
}
else if (sameString(dataFormat, BED_FORMAT))
{
/* minSizeT here and in liftOverChain.c/h has been renamed minChainT in liftOver.c */
ct = liftOverBed(oldTn.forCgi, chainHash,
minMatch, minBlocks, 0, minSizeQ,
minSizeT, 0,
fudgeThick, mapped, unmapped, multiple, NULL, &errCt);
}
else
/* programming error */
errAbort("ERROR: Unsupported data format: %s\n", dataFormat);
webNewSection("Results");
if (ct)
{
/* some records succesfully converted */
cgiParagraph("");
printf("Successfully converted %d record", ct);
printf("%s: ", ct > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi);
}
if (errCt)
{
/* some records not converted */
cgiParagraph("");
printf("Conversion failed on %d record", errCt);
printf("%s. ", errCt > 1 ? "s" : "");
printf("<A HREF=%s TARGET=_blank>Display failure file</A> \n",
unmappedTn.forCgi);
printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR);
puts("<P>Failed input regions:\n");
struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE);
puts("<BLOCKQUOTE><PRE>\n");
while (lineFileNext(errFile, &line, &lineSize))
puts(line);
lineFileClose(&errFile);
puts("</PRE></BLOCKQUOTE>\n");
}
if (sameString(dataFormat, POSITION_FORMAT) && multiple)
{
puts("<BLOCKQUOTE><PRE>\n");
puts("Note: multiple checkbox ignored since it is not supported for position format.");
puts("</PRE></BLOCKQUOTE>\n");
}
carefulClose(&unmapped);
}
webDataFormats();
webDownloads();
cartWebEnd();
}
