struct encodeExp *encodeExpLoadAll(char *fileName) /* Load all encodeExp from a whitespace-separated file. * Dispose of this with encodeExpFreeList(). */ { struct encodeExp *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[8]; while (lineFileRow(lf, row)) { el = encodeExpLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; }
struct encodeExp *encodeExpLoadAllByChar(char *fileName, char chopper) /* Load all encodeExp from a chopper separated file. * Dispose of this with encodeExpFreeList(). */ { struct encodeExp *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[8]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = encodeExpLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; }
struct encodeExp *encodeExpLoadByQuery(struct sqlConnection *conn, char *query) /* Load all encodeExp 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 encodeExpFreeList(). */ { struct encodeExp *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = encodeExpLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; }
void encodeExpToTab(char *outExp, char *outSeries, char *outResults) /* encodeExpToCvDb - Convert encode experiments table to a table more suitable for cvDb. */ { struct hash *optHash = optionalFieldsHash(); struct mdbObj *mdbList = getMdbList(metaDbs, ArraySize(metaDbs)); struct hash *mdbHash = mdbHashKeyedByExpId(mdbList); struct hash *seriesHash = hashNew(0); struct series *seriesList = NULL; verbose(1, "read %d mdb objects from %s in %d databases\n", mdbHash->elCount, metaTable, (int)ArraySize(metaDbs)); struct sqlConnection *expDbConn = sqlConnect(expDb); struct sqlConnection *cvDbConn = sqlConnect(cvDb); char query[256]; sqlSafef(query, sizeof(query), "select * from %s", expTable); struct sqlResult *sr = sqlGetResult(expDbConn, query); FILE *f = mustOpen(outExp, "w"); char **row; while ((row = sqlNextRow(sr)) != NULL) { /* Read in database structure. */ struct encodeExp *ee = encodeExpLoad(row); /* Much of the data we're processing comes from lists of the form * "a=aVal b=bVal c=cVal." We'll convert these to id's in the appropriate * tables and store the IDs in the optCol array declared below. */ int optColCount = ArraySize(expOptionalFields); int optCol[optColCount]; int i; for (i=0; i<optColCount; ++i) optCol[i] = 0; /* Convert var=val string in encodeExp.expVars into list of slPairs, and loop through it. */ struct slPair *varList = slPairListFromString(ee->expVars, TRUE); struct slPair *var; for (var = varList; var != NULL; var = var->next) { /* Figure out name of table and the term within that table. */ char *table = var->name; char *term = var->val; if (sameString(table, "antibody")) // Deal with antibody special case { if (sameString(term, "Control") || sameString(term, "Input") || sameString(term, "RevXlinkChromatin") || sameString(term, "ripInput")) { table = "control"; } } /* If it looks like we have a valid table and term, store result in * optCol array we'll output soon. */ struct hashEl *hel; if ((hel = hashLookup(optHash, table)) != NULL) { int id = lookupId(cvDbConn, table, term); if (id == 0) { warn("No id in cvDb for %s=%s\n", table, term); continue; } int optColIx = ptToInt(hel->val); optCol[optColIx] = id; } else verbose(2, "%s %s ?\n", table, term); } /* Now we want to process metaDb, which has some info encodeExp does not. */ char *composite = NULL; char ixAsString[16]; safef(ixAsString, sizeof(ixAsString), "%d", ee->ix); struct mdbObj *mdb = hashFindVal(mdbHash, ixAsString); if (mdb != NULL) { struct mdbVar *v; for (v = mdb->vars; v != NULL; v = v->next) { /* Look up table and term and change table name if need be */ char *table = v->var; char *term = v->val; if (sameString(table, "antibody")) table = "ab"; else if (sameString(table, "grant")) table = "grantee"; /* Squirrel away the ever-important composite term for later. */ if (sameString("composite", table)) composite = term; struct hashEl *hel; if ((hel = hashLookup(optHash, table)) != NULL) { int optColIx = ptToInt(hel->val); if (optCol[optColIx] == 0) // Only use mdb if encodeExp has no data. { int id = lookupId(cvDbConn, table, term); optCol[optColIx] = id; } } } } /* If we've got a composite, then make up a series record. */ if (composite != NULL) { assert(mdb != NULL); struct series *series = hashFindVal(seriesHash, composite); if (series == NULL) { series = seriesFromMdb(mdb, composite); hashAdd(seriesHash, composite, series); slAddHead(&seriesList, series); } } if (ee->accession != NULL) { /* Write out required fields. Order of required fields * here needs to follow order in expRequiredFields. */ fprintf(f, "%u", ee->ix); fprintf(f, "\t%s", ee->updateTime); fprintf(f, "\t%s", naForNull(composite)); fprintf(f, "\t%s", ee->accession); fprintf(f, "\t%d", lookupId(cvDbConn, "organism", ee->organism)); fprintf(f, "\t%d", lookupId(cvDbConn, "lab", ee->lab)); fprintf(f, "\t%d", lookupId(cvDbConn, "dataType", ee->dataType)); fprintf(f, "\t%d", lookupId(cvDbConn, "cellType", ee->cellType)); /* Now write out optional fields. */ for (i=0; i<optColCount; ++i) fprintf(f, "\t%d", optCol[i]); /* End output record. */ fprintf(f, "\n"); } } /* Write out series list to a separate file. */ slReverse(&seriesList); writeSeriesList(outSeries, seriesList); /* Write out results to a separate file. */ writeMdbListAsResults(mdbList, outResults); /* Clean up and go home. */ carefulClose(&f); sqlFreeResult(&sr); sqlDisconnect(&expDbConn); sqlDisconnect(&cvDbConn); }