3a63c684fc647b345d52e96147b3344453b3d28a
kate
  Fri Jul 31 10:12:14 2015 -0700
1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats.  3. Extend gtexInfo table.refs #15645

diff --git src/hg/lib/gtexTissueMedian.c src/hg/lib/gtexTissueMedian.c
new file mode 100644
index 0000000..de74fa7
--- /dev/null
+++ src/hg/lib/gtexTissueMedian.c
@@ -0,0 +1,158 @@
+/* gtexTissueMedian.c was originally generated by the autoSql program, which also 
+ * generated gtexTissueMedian.h and gtexTissueMedian.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 "gtexTissueMedian.h"
+
+
+
+char *gtexTissueMedianCommaSepFieldNames = "geneId,tissueCount,scores";
+
+struct gtexTissueMedian *gtexTissueMedianLoad(char **row)
+/* Load a gtexTissueMedian from row fetched with select * from gtexTissueMedian
+ * from database.  Dispose of this with gtexTissueMedianFree(). */
+{
+struct gtexTissueMedian *ret;
+
+AllocVar(ret);
+ret->tissueCount = sqlUnsigned(row[1]);
+ret->geneId = cloneString(row[0]);
+{
+int sizeOne;
+sqlFloatDynamicArray(row[2], &ret->scores, &sizeOne);
+assert(sizeOne == ret->tissueCount);
+}
+return ret;
+}
+
+struct gtexTissueMedian *gtexTissueMedianLoadAll(char *fileName) 
+/* Load all gtexTissueMedian from a whitespace-separated file.
+ * Dispose of this with gtexTissueMedianFreeList(). */
+{
+struct gtexTissueMedian *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileRow(lf, row))
+    {
+    el = gtexTissueMedianLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexTissueMedian *gtexTissueMedianLoadAllByChar(char *fileName, char chopper) 
+/* Load all gtexTissueMedian from a chopper separated file.
+ * Dispose of this with gtexTissueMedianFreeList(). */
+{
+struct gtexTissueMedian *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gtexTissueMedianLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexTissueMedian *gtexTissueMedianCommaIn(char **pS, struct gtexTissueMedian *ret)
+/* Create a gtexTissueMedian out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gtexTissueMedian */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->geneId = sqlStringComma(&s);
+ret->tissueCount = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->scores, ret->tissueCount);
+for (i=0; i<ret->tissueCount; ++i)
+    {
+    ret->scores[i] = sqlFloatComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void gtexTissueMedianFree(struct gtexTissueMedian **pEl)
+/* Free a single dynamically allocated gtexTissueMedian such as created
+ * with gtexTissueMedianLoad(). */
+{
+struct gtexTissueMedian *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->geneId);
+freeMem(el->scores);
+freez(pEl);
+}
+
+void gtexTissueMedianFreeList(struct gtexTissueMedian **pList)
+/* Free a list of dynamically allocated gtexTissueMedian's */
+{
+struct gtexTissueMedian *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gtexTissueMedianFree(&el);
+    }
+*pList = NULL;
+}
+
+void gtexTissueMedianOutput(struct gtexTissueMedian *el, FILE *f, char sep, char lastSep) 
+/* Print out gtexTissueMedian.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->tissueCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->tissueCount; ++i)
+    {
+    fprintf(f, "%g", el->scores[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+void gtexTissueMedianCreateTable(struct sqlConnection *conn, char *table)
+/* Create expression record format table of given name. */
+{
+char query[1024];
+
+sqlSafef(query, sizeof(query),
+"CREATE TABLE %s (\n"
+"    geneId varchar(255) not null,     # Gene identifier (ensembl)\n"
+"    tissueCount int unsigned not null,# Number of tissues\n"
+"    scores longblob not null,	       # Median expression levels for tissues (RPKM)\n"
+"              #Indices\n"
+"    PRIMARY KEY(geneId)\n"
+")\n",   table);
+sqlRemakeTable(conn, table, query);
+}
+