src/hg/makeDb/hgLoadSeq/hgLoadSeq.c 1.15

Index: src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/hgLoadSeq/hgLoadSeq.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 1000000 -r1.14 -r1.15
--- src/hg/makeDb/hgLoadSeq/hgLoadSeq.c	3 Sep 2008 19:19:44 -0000	1.14
+++ src/hg/makeDb/hgLoadSeq/hgLoadSeq.c	1 Oct 2009 07:50:03 -0000	1.15
@@ -1,216 +1,217 @@
 /* hgLoadSeq - load sequences into the seq/extFile tables. */
 
 #include "common.h"
 #include "options.h"
 #include "portable.h"
 #include "linefile.h"
 #include "hash.h"
 #include "fa.h"
 #include "hgRelate.h"
 
 static char const rcsid[] = "$Id$";
 
 /* command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {"abbr", OPTION_STRING},
     {"prefix", OPTION_STRING},
     {"replace", OPTION_BOOLEAN},
     {"test", OPTION_BOOLEAN},
     {"seqTbl", OPTION_STRING},
     {"extFileTbl", OPTION_STRING},
     {NULL, 0}
 };
 
 /* Command line options and defaults. */
 char *seqTbl = "seq";
 char *extFileTbl = "extFile";
 char *abbr = NULL;
 char *prefix = NULL;
 boolean test = FALSE;
 boolean replace = FALSE;
 
 char seqTableCreate[] =
 /* This keeps track of a sequence. */
 "create table %s ("
   "id int unsigned not null primary key," /* Unique ID across all tables. */
   "acc varchar(128) not null ,"	          /* seq  ID. */
   "size int unsigned not null,"           /* Size of sequence in bases. */
   "gb_date date not null,"                /* GenBank last modified date,
                                            * not used, for compatbility with older databases. */
   "extFile int unsigned not null,"        /* File it is in. */
   "file_offset bigint not null,"          /* Offset in file. */
   "file_size int unsigned not null,"      /* Size in file. */
   /* Extra indices. */
   "unique (acc))";
 
 boolean faSeekNextRecord(struct lineFile *faLf)
 /* Seeks to the next FA record.  Returns FALSE if seeks to EOF. */
 {
 char *faLine;
 int faLineSize;
 while (lineFileNext(faLf, &faLine, &faLineSize))
     {
     if (faLine[0] == '>')
 	return TRUE;
     }
 return FALSE;
 }
 
 void abbreviate(char *s, char *fluff)
 /* Cut out fluff from s. */
 {
 int len;
 if (s != NULL && fluff != NULL)
     {
     s = strstr(s, fluff);
     if (s != NULL)
        {
        len = strlen(fluff);
        strcpy(s, s+len);
        }
     }
 }
 
 boolean loadFaSeq(struct lineFile *faLf, HGID extFileId, FILE *seqTab,
                   struct sqlConnection* conn)
 /* Add next sequence in fasta file to tab file */
 {
 off_t faOffset, faEndOffset;
 int faSize;
 char *s, *faLine;
 int faLineSize, faNameSize;
 int dnaSize = 0;
 char faAcc[256], faAccBuf[513];
 HGID seqId = 0;
 int prefixLen = 0;
 
 /* Get Next FA record. */
 if (!lineFileNext(faLf, &faLine, &faLineSize))
     return FALSE;;
 if (faLine[0] != '>')
     internalErr();
 faOffset = faLf->bufOffsetInFile + faLf->lineStart;
 s = firstWordInLine(faLine+1);
 abbreviate(s, abbr);
 faNameSize = strlen(s);
 if (faNameSize == 0)
     errAbort("Missing accession line %d of %s", faLf->lineIx, faLf->fileName);
 if (prefix != NULL)
     prefixLen = strlen(prefix) + 1;
 if (strlen(faLine+1) + prefixLen >= sizeof(faAcc))
     errAbort("Fasta name too long line %d of %s", faLf->lineIx, faLf->fileName);
 faAcc[0] = 0;
 if (prefix != NULL)
     {
     strcat(faAcc, prefix);
     strcat(faAcc, "-");
     }
 strcat(faAcc, s);
 if (faSeekNextRecord(faLf))
     lineFileReuse(faLf);
 faEndOffset = faLf->bufOffsetInFile + faLf->lineStart;
 faSize = (int)(faEndOffset - faOffset); 
 
 /* add to tab file */
 seqId = hgNextId();
     
 /* note: sqlDate column is empty */
 fprintf(seqTab, "%u\t%s\t%d\t\t%u\t%lld\t%d\n",
         seqId, sqlEscapeTabFileString2(faAccBuf, faAcc),
         dnaSize, extFileId, (unsigned long long)faOffset, faSize);
 return TRUE;
 }
 
 void loadFa(char *faFile, struct sqlConnection *conn, FILE *seqTab)
 /* Add sequences in a fasta file to a seq table tab file */
 {
 HGID extFileId = test ? 0 : hgAddToExtFileTbl(faFile, conn, extFileTbl);
 struct lineFile *faLf = lineFileOpen(faFile, TRUE);
 unsigned count = 0;
 
 verbose(1, "Adding %s\n", faFile);
 
 /* Seek to first line starting with '>' in line file. */
 if (!faSeekNextRecord(faLf))
     errAbort("%s doesn't appear to be an .fa file\n", faLf->fileName);
 lineFileReuse(faLf);
 
 /* Loop around for each record of FA */
 while (loadFaSeq(faLf, extFileId, seqTab, conn))
     count++;
 
 verbose(1, "%u sequences\n", count);
 lineFileClose(&faLf);
 }
 
 void hgLoadSeq(char *database, int fileCount, char *fileNames[])
 /* Add a bunch of FA files to sequence and extFile tables of
  * database. */
 {
 struct sqlConnection *conn;
 int i;
 FILE *seqTab;
 
 if (!test)
     {
     conn = hgStartUpdate(database);
     char query[1024];
     safef(query, sizeof(query), seqTableCreate, seqTbl);
     sqlMaybeMakeTable(conn, seqTbl, query);
     }
 
 verbose(1, "Creating %s.tab file\n", seqTbl);
 seqTab = hgCreateTabFile(".", seqTbl);
 for (i=0; i<fileCount; ++i)
     {
     loadFa(fileNames[i], conn, seqTab);
     }
 if (!test)
     {
     unsigned opts = SQL_TAB_FILE_WARN_ON_ERROR;
     if (replace)
         opts |= SQL_TAB_REPLACE;
     verbose(1, "Updating %s table\n", seqTbl);
     hgLoadTabFileOpts(conn, ".", seqTbl, opts, &seqTab);
-    hgEndUpdate(&conn, "Add sequences");
+    hgEndUpdate(&conn, "Add sequences from %d files starting with %s", 
+    	fileCount, fileNames[0]);
     verbose(1, "All done\n");
     }
 }
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgLoadSeq - load browser database with sequence file info.\n"
   "usage:\n"
   "   hgLoadSeq [-abbr=junk] database file(s).fa\n"
   "This loads sequence file info only, it is not used for genbank data.\n"
   "\n"
   "Options:\n"
   "  -abbr=junk - remove junk from the start of each seq accession\n"
   "  -prefix=xxx - prepend \"xxx-\" to each seq accession\n"
   "  -replace - replace existing sequences with the same id\n"
   "  -seqTbl=tbl - use this table instead of seq\n"
   "  -extFileTbl=tbl - use this table instead of extFile\n"
   "  -test - do not load database table\n"
   );
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc < 2)
     usage();
 if ((optionExists("seqTbl") && !optionExists("extFileTbl"))
     || (!optionExists("seqTbl") && optionExists("extFileTbl")))
     errAbort("must specified both or neither of -seqTbl and -extFileTbl");
 seqTbl = optionVal("seqTbl", seqTbl);
 extFileTbl = optionVal("extFileTbl", extFileTbl);
 abbr = optionVal("abbr", NULL);
 prefix = optionVal("prefix", NULL);
 replace = optionExists("replace");
 test = optionExists("test");
 hgLoadSeq(argv[1], argc-2, argv+2);
 return 0;
 }