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/gtexSampleData.c src/hg/lib/gtexSampleData.c
new file mode 100644
index 0000000..67a38ac
--- /dev/null
+++ src/hg/lib/gtexSampleData.c
@@ -0,0 +1,155 @@
+/* gtexSampleData.c was originally generated by the autoSql program, which also 
+ * generated gtexSampleData.h and gtexSampleData.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 "gtexSampleData.h"
+
+
+
+char *gtexSampleDataCommaSepFieldNames = "geneId,sample,tissue,score";
+
+void gtexSampleDataStaticLoad(char **row, struct gtexSampleData *ret)
+/* Load a row from gtexSampleData table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->geneId = row[0];
+ret->sample = row[1];
+ret->tissue = row[2];
+ret->score = sqlFloat(row[3]);
+}
+
+struct gtexSampleData *gtexSampleDataLoad(char **row)
+/* Load a gtexSampleData from row fetched with select * from gtexSampleData
+ * from database.  Dispose of this with gtexSampleDataFree(). */
+{
+struct gtexSampleData *ret;
+
+AllocVar(ret);
+ret->geneId = cloneString(row[0]);
+ret->sample = cloneString(row[1]);
+ret->tissue = cloneString(row[2]);
+ret->score = sqlFloat(row[3]);
+return ret;
+}
+
+struct gtexSampleData *gtexSampleDataLoadAll(char *fileName) 
+/* Load all gtexSampleData from a whitespace-separated file.
+ * Dispose of this with gtexSampleDataFreeList(). */
+{
+struct gtexSampleData *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[4];
+
+while (lineFileRow(lf, row))
+    {
+    el = gtexSampleDataLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexSampleData *gtexSampleDataLoadAllByChar(char *fileName, char chopper) 
+/* Load all gtexSampleData from a chopper separated file.
+ * Dispose of this with gtexSampleDataFreeList(). */
+{
+struct gtexSampleData *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[4];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gtexSampleDataLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexSampleData *gtexSampleDataCommaIn(char **pS, struct gtexSampleData *ret)
+/* Create a gtexSampleData out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gtexSampleData */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->geneId = sqlStringComma(&s);
+ret->sample = sqlStringComma(&s);
+ret->tissue = sqlStringComma(&s);
+ret->score = sqlFloatComma(&s);
+*pS = s;
+return ret;
+}
+
+void gtexSampleDataFree(struct gtexSampleData **pEl)
+/* Free a single dynamically allocated gtexSampleData such as created
+ * with gtexSampleDataLoad(). */
+{
+struct gtexSampleData *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->geneId);
+freeMem(el->sample);
+freeMem(el->tissue);
+freez(pEl);
+}
+
+void gtexSampleDataFreeList(struct gtexSampleData **pList)
+/* Free a list of dynamically allocated gtexSampleData's */
+{
+struct gtexSampleData *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gtexSampleDataFree(&el);
+    }
+*pList = NULL;
+}
+
+void gtexSampleDataOutput(struct gtexSampleData *el, FILE *f, char sep, char lastSep) 
+/* Print out gtexSampleData.  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);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->sample);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->tissue);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%g", el->score);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+void gtexSampleDataCreateTable(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"
+"    sample varchar(255) not null,     # GTEx sample identifier\n"
+"    tissue varchar(255) not null,     # Tissue name\n"
+"    score float not null,	# Expression level (RPKM)\n"
+"              #Indices\n"
+"    PRIMARY KEY(geneId)\n"
+")\n",   table);
+sqlRemakeTable(conn, table, query);
+}