4418dae2476e397d9c03c1301e573e2c45b1a58e
hiram
  Fri Feb 10 12:16:43 2023 -0800
adding asmEquivalent functions to this library no redmine

diff --git src/hg/lib/asmEquivalent.c src/hg/lib/asmEquivalent.c
index 64896b4..3971aadd 100644
--- src/hg/lib/asmEquivalent.c
+++ src/hg/lib/asmEquivalent.c
@@ -1,25 +1,27 @@
 /* asmEquivalent.c was originally generated by the autoSql program, which also 
  * generated asmEquivalent.h and asmEquivalent.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 "asmEquivalent.h"
 
+#include "hdb.h"
+
 
 
 char *asmEquivalentCommaSepFieldNames = "source,destination,sourceAuthority,destinationAuthority,matchCount,sourceCount,destinationCount";
 
 /* definitions for sourceAuthority column */
 static char *values_sourceAuthority[] = {"ensembl", "ucsc", "genbank", "refseq", NULL};
 static struct hash *valhash_sourceAuthority = NULL;
 
 /* definitions for destinationAuthority column */
 static char *values_destinationAuthority[] = {"ensembl", "ucsc", "genbank", "refseq", NULL};
 static struct hash *valhash_destinationAuthority = NULL;
 
 void asmEquivalentStaticLoad(char **row, struct asmEquivalent *ret)
 /* Load a row from asmEquivalent table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
@@ -52,31 +54,31 @@
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void asmEquivalentSaveToDb(struct sqlConnection *conn, struct asmEquivalent *el, char *tableName, int updateSize)
 /* Save asmEquivalent 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 = dyStringNew(updateSize);
-sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',(null),(null),%lld,%lld,%lld)",
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%d,%d,%lld,%lld,%lld)",
 	tableName,  el->source,  el->destination,  el->sourceAuthority,  el->destinationAuthority,  el->matchCount,  el->sourceCount,  el->destinationCount);
 sqlUpdate(conn, update->string);
 dyStringFree(&update);
 }
 
 struct asmEquivalent *asmEquivalentLoad(char **row)
 /* Load a asmEquivalent from row fetched with select * from asmEquivalent
  * from database.  Dispose of this with asmEquivalentFree(). */
 {
 struct asmEquivalent *ret;
 
 AllocVar(ret);
 ret->source = cloneString(row[0]);
 ret->destination = cloneString(row[1]);
 ret->sourceAuthority = sqlEnumParse(row[2], values_sourceAuthority, &valhash_sourceAuthority);
@@ -241,15 +243,65 @@
 fprintf(f,"sourceCount");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%lld", el->sourceCount);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"destinationCount");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%lld", el->destinationCount);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
+char *asmEquivalentUcscToNCBI(char *ucscName)
+/* check if there is a RefSeq/GenBank equivalent to this UCSC assembly name.
+ *    If RefSeq exists, return that first, else if GenBank than return that.
+ * No checking of sequence match counts in this first implementation,
+ *    therefore, could be a fuzzy match, and since it is returning only the
+ *    first one, it might not be the best match.  Could add more specifics
+ *    later to get better match.
+ */
+{
+char *ret = NULL;
+if (ucscName == NULL)
+    return ret;
+
+struct sqlConnection *conn = hAllocConn("hgFixed");
+if (!conn)
+    return ret;
+
+if (!sqlTableExists(conn, "asmEquivalent"))
+    {
+    hFreeConn(&conn);
+    return ret;
+    }
+
+char buffer[4096];
+
+sqlSafef(buffer, sizeof buffer, "SELECT destination FROM asmEquivalent WHERE sourceAuthority='ucsc' AND destinationAuthority='refseq' AND source='%s' LIMIT 1", ucscName);
+char *sqlAnswer = sqlQuickString(conn, buffer);
+if (isEmpty(sqlAnswer))
+    {
+    sqlSafef(buffer, sizeof buffer, "SELECT destination FROM asmEquivalent WHERE sourceAuthority='ucsc' AND destinationAuthority='genbank' AND source='%s' LIMIT 1", ucscName);
+    sqlAnswer = sqlQuickString(conn, buffer);
+    }
+hFreeConn(&conn);
+
+/* if there is a result, for example: GCA_000001405.28_GRCh38.p13
+ *    want to return only: GCA_000001405.28
+ */
+if (isNotEmpty(sqlAnswer))
+    {
+    char *words[3];
+    int wordCount = 0;
+    wordCount = chopString(sqlAnswer, "_", words, ArraySize(words));
+    if (3 != wordCount)	/* something wrong with this answer */
+       return ret;
+    safef(buffer, sizeof(buffer), "%s_%s", words[0], words[1]);
+    ret = cloneString(buffer);
+    }
+
+return ret;
+}