/* hgLoadNet - Load a chain/net file into database. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "obscure.h" #include "hash.h" #include "jksql.h" #include "dystring.h" #include "bed.h" #include "hdb.h" #include "chainNet.h" #include "options.h" /* Command line switches. */ boolean noBin = FALSE; /* Suppress bin field. */ boolean oldTable = FALSE; /* Don't redo table. */ boolean warnFlag = FALSE; /* load even with missing fields */ boolean warned = FALSE; char *sqlTable = NULL; /* Read table from this .sql if non-NULL. */ char *qPrefix = NULL; /* Prepend prefix and "-" to query name */ boolean test = FALSE; static struct optionSpec optionSpecs[] = { {"noBin", OPTION_BOOLEAN}, {"oldTable", OPTION_BOOLEAN}, {"warn", OPTION_BOOLEAN}, {"sqlTable", OPTION_STRING}, {"qPrefix", OPTION_STRING}, {"test", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "hgLoadNet - Load a generic net file into database\n" "usage:\n" " hgLoadNet database track files(s).net\n" "options:\n" " -noBin suppress bin field\n" " -oldTable add to existing table\n" " -sqlTable=table.sql Create table from .sql file\n" " -qPrefix=xxx prepend \"xxx-\" to query name\n" " -warn load even with missing fields\n" " -test suppress loading table\n" ); } void loadDatabase(char *database, char *tab, char *track) /* Load database from tab file. */ { struct sqlConnection *conn = sqlConnect(database); struct dyString *dy = dyStringNew(1024); /* First make table definition. */ if (sqlTable != NULL) { /* Read from file. */ char *sql, *s; readInGulp(sqlTable, &sql, NULL); /* Chop of end-of-statement semicolon if need be. */ s = strchr(sql, ';'); if (s != NULL) *s = 0; sqlRemakeTable(conn, track, sql); freez(&sql); } else if (!oldTable) { /* Create definition statement. */ verbose(1, "Creating table definition for %s\n", track); sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track); if (!noBin) sqlDyStringPrintf(dy, " bin smallint unsigned not null,\n"); sqlDyStringPrintf(dy, " level int unsigned not null,\n" " tName varchar(255) not null,\n" " tStart int unsigned not null,\n" " tEnd int unsigned not null,\n" " strand char(1) not null,\n" " qName varchar(255) not null,\n" " qStart int unsigned not null,\n" " qEnd int unsigned not null,\n" " chainId int unsigned not null,\n" " ali int unsigned not null,\n" " score double not null,\n" " qOver int not null, \n" " qFar int not null, \n" " qDup int not null, \n" " type varchar(255) not null,\n" " tN int not null, \n" " qN int not null, \n" " tR int not null, \n" " qR int not null, \n" " tNewR int not null, \n" " qNewR int not null, \n" " tOldR int not null, \n" " qOldR int not null, \n" " tTrf int not null, \n" " qTrf int not null, \n" "#Indices\n"); if (!noBin) sqlDyStringPrintf(dy, " INDEX(tName(16),bin),\n"); sqlDyStringPrintf(dy, " INDEX(tName(16),tStart)\n" ")\n"); sqlRemakeTable(conn, track, dy->string); } dyStringClear(dy); sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track); verbose(1, "Loading %s into %s\n", track, database); sqlUpdate(conn, dy->string); /* add a comment to the history table and finish up connection */ hgHistoryComment(conn, "Loaded net table %s", track); sqlDisconnect(&conn); } void cnWriteTables(char *chrom, struct cnFill *fillList, FILE *f, int depth) /* Recursively write out fill and gap lists. */ { char qName[64]; struct cnFill *fill; for (fill = fillList; fill != NULL; fill = fill->next) { if (fill->chainId != 0) { if (fill->type == NULL) errAbort("No type field, please run netSyntenic on input"); if (fill->tN < 0) { if (warnFlag) { if (!warned) { fprintf(stderr, "Warning: missing fields\n"); warned = TRUE; } } else errAbort("Missing fields. Please run netClass on input"); } } if (fill->score < 0) fill->score = 0; if (!noBin) fprintf(f, "%d\t", hFindBin(fill->tStart, fill->tStart + fill->tSize)); qName[0] = 0; if (qPrefix != NULL) { strcat(qName, qPrefix); strcat(qName, "-"); } strcat(qName, fill->qName); fprintf(f, "%d\t", depth); fprintf(f, "%s\t", chrom); fprintf(f, "%d\t", fill->tStart); fprintf(f, "%d\t", fill->tStart + fill->tSize); fprintf(f, "%c\t", fill->qStrand); fprintf(f, "%s\t", qName); fprintf(f, "%d\t", fill->qStart); fprintf(f, "%d\t", fill->qStart + fill->qSize); fprintf(f, "%d\t", fill->chainId); fprintf(f, "%d\t", fill->ali); fprintf(f, "%1.1f\t", fill->score); fprintf(f, "%d\t", fill->qOver); fprintf(f, "%d\t", fill->qFar); fprintf(f, "%d\t", fill->qDup); fprintf(f, "%s\t", (fill->type == NULL ? "gap" : fill->type)); fprintf(f, "%d\t", fill->tN); fprintf(f, "%d\t", fill->qN); fprintf(f, "%d\t", fill->tR); fprintf(f, "%d\t", fill->qR); fprintf(f, "%d\t", fill->tNewR); fprintf(f, "%d\t", fill->qNewR); fprintf(f, "%d\t", fill->tOldR); fprintf(f, "%d\t", fill->qOldR); fprintf(f, "%d\t", fill->tTrf); fprintf(f, "%d\n", fill->qTrf); if (fill->children) cnWriteTables(chrom, fill->children, f, depth+1); } } void hgLoadNet(char *database, char *track, int netCount, char *netFiles[]) /* hgLoadNet - Load a net file into database. */ { int i; struct lineFile *lf ; struct chainNet *net; char alignFileName[] ="align.tab"; FILE *alignFile = mustOpen(alignFileName,"w"); for (i=0; iname); cnWriteTables(net->name,net->fillList, alignFile, 1); chainNetFree(&net); } lineFileClose(&lf); } fclose(alignFile); if (!test) { loadDatabase(database, alignFileName, track); remove(alignFileName); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc < 4) usage(); noBin = optionExists("noBin"); oldTable = optionExists("oldTable"); warnFlag = optionExists("warn"); sqlTable = optionVal("sqlTable", NULL); qPrefix = optionVal("qPrefix", NULL); test = optionExists("test"); hgLoadNet(argv[1], argv[2], argc-3, argv+3); return 0; }