void webDownloads()
{
webNewSection("Command Line Tool");
cgiParagraph(
"To lift genome annotations locally on Linux systems, download the "
"<A HREF=\"http://hgdownload.cse.ucsc.edu/admin/exe/\">"
"<I>liftOver</I></A> executable and the appropriate "
"<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html#liftover\">"
"chain file</A>."
" Run <I>liftOver</I> with no arguments to see the usage message.\n");
}
void makeForm(struct slName *dbs)
/* If the button wasn't pressed already, show it. */
{
struct slName *cur;
cgiParagraph("Pressing the button below will trigger an update to the MGC RTDB database:");
/* HTML form */
puts("<FORM ACTION=\"../cgi-bin/rtdbWebUpdate\" METHOD=\"POST\" "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
for (cur = dbs; cur != NULL; cur = cur->next)
{
cgiMakeRadioButton("db", cur->name, FALSE);
printf(" %s\n<BR>\n", cur->name);
}
puts("<BR>\n");
cgiMakeButton("RTDBSubmit","Update RTDB");
cartSaveSession(cart);
puts("</FORM>");
}
void webMain(struct liftOverChain *chain, char *dataFormat, boolean multiple)
/* set up page for entering data */
{
struct dbDb *dbList;
char *fromOrg = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb);
cgiParagraph(
"This tool converts genome coordinates and genome annotation files "
"between assemblies. "
"The input data can be pasted into the text box, or uploaded from a file. "
"If a pair of assemblies cannot be selected from the pull-down menus,"
" a direct lift between them is unavailable. "
"However, a sequential lift may be possible. "
"Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, "
"Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9. "
"");
/* create HMTL form */
puts("<FORM ACTION=\"../cgi-bin/hgLiftOver\" METHOD=\"POST\" "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
/* create HTML table for layout purposes */
puts("\n<TABLE WIDTH=\"100%%\">\n");
/* top two rows -- genome and assembly menus */
cgiSimpleTableRowStart();
cgiTableField("Original Genome: ");
cgiTableField("Original Assembly: ");
cgiTableField("New Genome: ");
cgiTableField("New Assembly: ");
cgiTableRowEnd();
cgiSimpleTableRowStart();
/* genome */
cgiSimpleTableFieldStart();
dbList = hGetLiftOverFromDatabases();
printSomeGenomeListHtmlNamed(HGLFT_FROMORG_VAR, chain->fromDb, dbList, onChange);
cgiTableFieldEnd();
/* from assembly */
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(chain->fromDb, dbList, HGLFT_FROMDB_VAR,
TRUE, onChange);
cgiTableFieldEnd();
/* to assembly */
cgiSimpleTableFieldStart();
dbDbFreeList(&dbList);
dbList = hGetLiftOverToDatabases(chain->fromDb);
printLiftOverGenomeList(HGLFT_TOORG_VAR, chain->toDb, dbList, onChange);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(chain->toDb, dbList, HGLFT_TODB_VAR, TRUE, "");
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
cgiParagraph(" ");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum ratio of bases that must remap:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeDoubleVar(HGLFT_MINMATCH,chain->minMatch,6);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum chain size in target:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeIntVar(HGLFT_MINSIZET,chain->minSizeT,4);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum hit size in query:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeIntVar(HGLFT_MINSIZEQ,chain->minSizeQ,4);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Allow multiple output regions:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeCheckBox(HGLFT_MULTIPLE,multiple);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Min ratio of alignment blocks/exons that must map:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeDoubleVar(HGLFT_MINBLOCKS,chain->minBlocks,6);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeCheckBox(HGLFT_FUDGETHICK,(chain->fudgeThick[0]=='Y') ? TRUE : FALSE);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* next row -- file format menu */
cgiParagraph(
" For descriptions of the supported data formats, see the bottom of this page.");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiTableField("Data Format: ");
cgiSimpleTableFieldStart();
cgiMakeDropList(HGLFT_DATAFORMAT_VAR,
formatList, sizeof(formatList)/sizeof (char*) - 1, dataFormat);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* text box and two buttons (submit, reset) */
cgiParagraph(" Paste in data:\n");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeTextArea(HGLFT_USERDATA_VAR, cartCgiUsualString(cart, HGLFT_USERDATA_VAR, NULL), 10, 80);
cgiTableFieldEnd();
/* right element of table is a nested table
* with two buttons stacked on top of each other */
cgiSimpleTableFieldStart();
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeSubmitButton();
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeClearButton("mainForm", HGLFT_USERDATA_VAR);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* next row -- file upload controls */
cgiParagraph(" Or upload data from a file:");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
printf("<TD><INPUT TYPE=FILE NAME=\"%s\"></TD>\n", HGLFT_DATAFILE_VAR);
puts("<TD><INPUT TYPE=SUBMIT NAME=SubmitFile VALUE=\"Submit File\"></TD>\n");
cgiTableRowEnd();
cgiTableEnd();
printf("<input type=\"hidden\" name=\"%s\" value=\"0\">\n",
HGLFT_REFRESHONLY_VAR);
puts("</FORM>\n");
cartSaveSession(cart);
puts("</FORM>");
freeMem(fromOrg);
freeMem(toOrg);
}
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();
}
