c9f02c74337b661effebb021028f73d7a1316565
kate
  Tue Feb 17 21:42:06 2015 -0800
First cut loader of GTEX gene track.  Enough here to test track display. refs #13504

diff --git src/hg/lib/gtexGeneBed.c src/hg/lib/gtexGeneBed.c
new file mode 100644
index 0000000..d1e4557
--- /dev/null
+++ src/hg/lib/gtexGeneBed.c
@@ -0,0 +1,212 @@
+/* gtexGeneBed.c was originally generated by the autoSql program, which also 
+ * generated gtexGeneBed.h and gtexGeneBed.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 "gtexGeneBed.h"
+
+
+
+char *gtexGeneBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,geneId,transcriptId,transcriptClass,expCount,expScores";
+
+struct gtexGeneBed *gtexGeneBedLoad(char **row)
+/* Load a gtexGeneBed from row fetched with select * from gtexGeneBed
+ * from database.  Dispose of this with gtexGeneBedFree(). */
+{
+struct gtexGeneBed *ret;
+
+AllocVar(ret);
+ret->expCount = sqlUnsigned(row[9]);
+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->geneId = cloneString(row[6]);
+ret->transcriptId = cloneString(row[7]);
+ret->transcriptClass = cloneString(row[8]);
+{
+int sizeOne;
+sqlFloatDynamicArray(row[10], &ret->expScores, &sizeOne);
+assert(sizeOne == ret->expCount);
+}
+return ret;
+}
+
+struct gtexGeneBed *gtexGeneBedLoadAll(char *fileName) 
+/* Load all gtexGeneBed from a whitespace-separated file.
+ * Dispose of this with gtexGeneBedFreeList(). */
+{
+struct gtexGeneBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[11];
+
+while (lineFileRow(lf, row))
+    {
+    el = gtexGeneBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexGeneBed *gtexGeneBedLoadAllByChar(char *fileName, char chopper) 
+/* Load all gtexGeneBed from a chopper separated file.
+ * Dispose of this with gtexGeneBedFreeList(). */
+{
+struct gtexGeneBed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[11];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gtexGeneBedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gtexGeneBed *gtexGeneBedCommaIn(char **pS, struct gtexGeneBed *ret)
+/* Create a gtexGeneBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gtexGeneBed */
+{
+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->geneId = sqlStringComma(&s);
+ret->transcriptId = sqlStringComma(&s);
+ret->transcriptClass = sqlStringComma(&s);
+ret->expCount = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->expScores, ret->expCount);
+for (i=0; i<ret->expCount; ++i)
+    {
+    ret->expScores[i] = sqlFloatComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void gtexGeneBedFree(struct gtexGeneBed **pEl)
+/* Free a single dynamically allocated gtexGeneBed such as created
+ * with gtexGeneBedLoad(). */
+{
+struct gtexGeneBed *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->geneId);
+freeMem(el->transcriptId);
+freeMem(el->transcriptClass);
+freeMem(el->expScores);
+freez(pEl);
+}
+
+void gtexGeneBedFreeList(struct gtexGeneBed **pList)
+/* Free a list of dynamically allocated gtexGeneBed's */
+{
+struct gtexGeneBed *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gtexGeneBedFree(&el);
+    }
+*pList = NULL;
+}
+
+void gtexGeneBedOutput(struct gtexGeneBed *el, FILE *f, char sep, char lastSep) 
+/* Print out gtexGeneBed.  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);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptClass);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->expCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->expCount; ++i)
+    {
+    fprintf(f, "%g", el->expScores[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+void gtexGeneBedCreateTable(struct sqlConnection *conn, char *table)
+/* Create expression record format table of given name. */
+{
+char query[1024];
+
+sqlSafef(query, sizeof(query),
+"CREATE TABLE %s (\n"
+"   chrom varchar(255) not null,	# Reference sequence chromosome or scaffold\n"
+"   chromStart int unsigned not null,	# Start position in chromosome\n"
+"   chromEnd int unsigned not null,	# End position in chromosome\n"
+"   name varchar(255) not null,	# Gene symbol\n"
+"   score int unsigned not null,	# Score from 0-1000\n"
+"   strand char(1) not null,	# + or - for strand\n"
+"   geneId varchar(255) not null,	# Ensembl gene ID, referenced in GTEx data tables\n"
+"   transcriptId varchar(255) not null,	# Ensembl ID of Canonical transcript; determines genomic position\n"
+"   transcriptClass varchar(255) not null,	# GENCODE transcript class (coding, nonCoding, pseudo)\n"
+"   expCount int unsigned not null,	# Number of experiment values\n"
+"   expScores longblob not null,	# Comma separated list of experiment scores\n"
+          "#Indices\n"
+"   PRIMARY KEY(geneId)\n"
+")\n",
+    table);
+sqlRemakeTable(conn, table, query);
+}