ba22bbbe65670b6378e16e7d60a214102e600a8f
kate
  Thu Jun 30 19:10:06 2016 -0700
Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)

diff --git src/hg/lib/gtexAse.c src/hg/lib/gtexAse.c
new file mode 100644
index 0000000..eccc601
--- /dev/null
+++ src/hg/lib/gtexAse.c
@@ -0,0 +1,214 @@
+/* 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";
+
+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->coverage = sqlFloat(row[10]);
+ret->samples = sqlUnsigned(row[11]);
+}
+
+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);
+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->coverage = sqlFloat(row[10]);
+ret->samples = sqlUnsigned(row[11]);
+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];
+
+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];
+
+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->coverage = sqlFloatComma(&s);
+ret->samples = sqlUnsignedComma(&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);
+fputc(sep,f);
+fprintf(f, "%g", el->ASE);
+fputc(sep,f);
+fprintf(f, "%g", el->coverage);
+fputc(sep,f);
+fprintf(f, "%u", el->samples);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+