965d1048e8671fb3a5630fe75deb88f24df386d7
kate
  Wed Aug 13 15:01:59 2014 -0700
Expand schema for GTex.  Create tissue short names and use these in sample and data tables. refs #13504
diff --git src/hg/lib/gtexTissueData.c src/hg/lib/gtexTissueData.c
new file mode 100644
index 0000000..4bae523
--- /dev/null
+++ src/hg/lib/gtexTissueData.c
@@ -0,0 +1,158 @@
+/* gtexTissueData.c was originally generated by the autoSql program, which also 
+ * generated gtexTissueData.h and gtexTissueData.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 "gtexTissueData.h"
+
+
+
+char *gtexTissueDataCommaSepFieldNames = "geneId,tissueCount,scores";
+
+struct gtexTissueData *gtexTissueDataLoad(char **row)
+/* Load a gtexTissueData from row fetched with select * from gtexTissueData
+ * from database.  Dispose of this with gtexTissueDataFree(). */
+{
+struct gtexTissueData *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 gtexTissueData *gtexTissueDataLoadAll(char *fileName) 
+/* Load all gtexTissueData from a whitespace-separated file.
+ * Dispose of this with gtexTissueDataFreeList(). */
+{
+struct gtexTissueData *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileRow(lf, row))
+    {
+    el = gtexTissueDataLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexTissueData *gtexTissueDataLoadAllByChar(char *fileName, char chopper) 
+/* Load all gtexTissueData from a chopper separated file.
+ * Dispose of this with gtexTissueDataFreeList(). */
+{
+struct gtexTissueData *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gtexTissueDataLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexTissueData *gtexTissueDataCommaIn(char **pS, struct gtexTissueData *ret)
+/* Create a gtexTissueData out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gtexTissueData */
+{
+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 gtexTissueDataFree(struct gtexTissueData **pEl)
+/* Free a single dynamically allocated gtexTissueData such as created
+ * with gtexTissueDataLoad(). */
+{
+struct gtexTissueData *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->geneId);
+freeMem(el->scores);
+freez(pEl);
+}
+
+void gtexTissueDataFreeList(struct gtexTissueData **pList)
+/* Free a list of dynamically allocated gtexTissueData's */
+{
+struct gtexTissueData *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gtexTissueDataFree(&el);
+    }
+*pList = NULL;
+}
+
+void gtexTissueDataOutput(struct gtexTissueData *el, FILE *f, char sep, char lastSep) 
+/* Print out gtexTissueData.  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 gtexTissueDataCreateTable(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);
+}
+