013ccd312d93bfb526241f9d81c4327a3b169b2e
kate
  Tue Aug 9 14:52:59 2016 -0700
Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table.  Generalize the new hub as GTex analysis.

diff --git src/hg/lib/gtexAse.c src/hg/lib/gtexAse.c
index eccc601..ecd17e9 100644
--- src/hg/lib/gtexAse.c
+++ src/hg/lib/gtexAse.c
@@ -1,214 +1,244 @@
 /* gtexAse.c was originally generated by the autoSql program, which also 
  * generated gtexAse.h and gtexAse.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "gtexAse.h"
 
 
 
-char *gtexAseCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,rgb,ASE,coverage,samples";
+char *gtexAseCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,medianASE,coverage,samples,donors,minASE,q1ASE,q3ASE,maxASE,stdASE";
 
 void gtexAseStaticLoad(char **row, struct gtexAse *ret)
 /* Load a row from gtexAse table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
-ret->rgb = sqlUnsigned(row[8]);
-ret->ASE = sqlFloat(row[9]);
+ret->itemRgb = sqlUnsigned(row[8]);
+ret->medianASE = sqlFloat(row[9]);
 ret->coverage = sqlFloat(row[10]);
 ret->samples = sqlUnsigned(row[11]);
+ret->donors = sqlUnsigned(row[12]);
+ret->minASE = sqlFloat(row[13]);
+ret->q1ASE = sqlFloat(row[14]);
+ret->q3ASE = sqlFloat(row[15]);
+ret->maxASE = sqlFloat(row[16]);
+ret->stdASE = sqlFloat(row[17]);
 }
 
 struct gtexAse *gtexAseLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all gtexAse from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with gtexAseFreeList(). */
 {
 struct gtexAse *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gtexAseLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gtexAseSaveToDb(struct sqlConnection *conn, struct gtexAse *el, char *tableName, int updateSize)
 /* Save gtexAse as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. This function automatically escapes quoted strings for mysql. */
 {
 struct dyString *update = newDyString(updateSize);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%g,%g,%u)", 
-	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->rgb,  el->ASE,  el->coverage,  el->samples);
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%g,%g,%u,%u,%g,%g,%g,%g,%g)", 
+	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->itemRgb,  el->medianASE,  el->coverage,  el->samples,  el->donors,  el->minASE,  el->q1ASE,  el->q3ASE,  el->maxASE,  el->stdASE);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 struct gtexAse *gtexAseLoad(char **row)
 /* Load a gtexAse from row fetched with select * from gtexAse
  * from database.  Dispose of this with gtexAseFree(). */
 {
 struct gtexAse *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
-ret->rgb = sqlUnsigned(row[8]);
-ret->ASE = sqlFloat(row[9]);
+ret->itemRgb = sqlUnsigned(row[8]);
+ret->medianASE = sqlFloat(row[9]);
 ret->coverage = sqlFloat(row[10]);
 ret->samples = sqlUnsigned(row[11]);
+ret->donors = sqlUnsigned(row[12]);
+ret->minASE = sqlFloat(row[13]);
+ret->q1ASE = sqlFloat(row[14]);
+ret->q3ASE = sqlFloat(row[15]);
+ret->maxASE = sqlFloat(row[16]);
+ret->stdASE = sqlFloat(row[17]);
 return ret;
 }
 
 struct gtexAse *gtexAseLoadAll(char *fileName) 
 /* Load all gtexAse from a whitespace-separated file.
  * Dispose of this with gtexAseFreeList(). */
 {
 struct gtexAse *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[12];
+char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = gtexAseLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexAse *gtexAseLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexAse from a chopper separated file.
  * Dispose of this with gtexAseFreeList(). */
 {
 struct gtexAse *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[12];
+char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexAseLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexAse *gtexAseCommaIn(char **pS, struct gtexAse *ret)
 /* Create a gtexAse out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexAse */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
-ret->rgb = sqlUnsignedComma(&s);
-ret->ASE = sqlFloatComma(&s);
+ret->itemRgb = sqlUnsignedComma(&s);
+ret->medianASE = sqlFloatComma(&s);
 ret->coverage = sqlFloatComma(&s);
 ret->samples = sqlUnsignedComma(&s);
+ret->donors = sqlUnsignedComma(&s);
+ret->minASE = sqlFloatComma(&s);
+ret->q1ASE = sqlFloatComma(&s);
+ret->q3ASE = sqlFloatComma(&s);
+ret->maxASE = sqlFloatComma(&s);
+ret->stdASE = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexAseFree(struct gtexAse **pEl)
 /* Free a single dynamically allocated gtexAse such as created
  * with gtexAseLoad(). */
 {
 struct gtexAse *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freez(pEl);
 }
 
 void gtexAseFreeList(struct gtexAse **pList)
 /* Free a list of dynamically allocated gtexAse's */
 {
 struct gtexAse *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexAseFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexAseOutput(struct gtexAse *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexAse.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
-fprintf(f, "%u", el->rgb);
+fprintf(f, "%u", el->itemRgb);
 fputc(sep,f);
-fprintf(f, "%g", el->ASE);
+fprintf(f, "%g", el->medianASE);
 fputc(sep,f);
 fprintf(f, "%g", el->coverage);
 fputc(sep,f);
 fprintf(f, "%u", el->samples);
+fputc(sep,f);
+fprintf(f, "%u", el->donors);
+fputc(sep,f);
+fprintf(f, "%g", el->minASE);
+fputc(sep,f);
+fprintf(f, "%g", el->q1ASE);
+fputc(sep,f);
+fprintf(f, "%g", el->q3ASE);
+fputc(sep,f);
+fprintf(f, "%g", el->maxASE);
+fputc(sep,f);
+fprintf(f, "%g", el->stdASE);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */