d57e88e244a6f7372791a93f52b1f4b1628801ff braney Wed Jul 15 08:38:34 2020 -0700 oops.. another place that references gff.h diff --git src/hg/lib/tests/genePredTester.c src/hg/lib/tests/genePredTester.c index 15c4ff5..773b9e3 100644 --- src/hg/lib/tests/genePredTester.c +++ src/hg/lib/tests/genePredTester.c @@ -1,434 +1,434 @@ /* genePredTester - test program for genePred and genePredReader */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "genePred.h" #include "genePredReader.h" #include "options.h" #include "psl.h" #include "gff.h" #include "genbank.h" #include "localmem.h" #include "hash.h" #include "linefile.h" #include "jksql.h" #include "binRange.h" #include "verbose.h" void usage(char *msg) /* Explain usage and exit. */ { errAbort( "%s\n\n" "genePredTester - test program for genePred and genePredReader\n" "\n" "Usage:\n" " genePredTester [options] task [args...]\n" "\n" "Tasks and arguments:\n" "\n" "o readTable db table\n" " Read rows from db.table into genePred objects, determining the\n" " columns dynamically. If -output is specified, the objects are\n" " written to that file. Field name columns are ignored.\n" "\n" "o loadTable db table gpFile\n" " Create and load the specified table from gbFile. Field command options\n" " defined optional columns in file.\n" "\n" "o readFile gpFile\n" " Read rows from the tab-separated file, Field command options\n" " defined optional columns in file. If -output is specified, the\n" " objects are written to that file.\n" "\n" "o fromPsl pslFile cdsFile \n" " Create genePred objects from PSL.If -output is specified, the\n" " objects are written to that file.\n" "\n" "o fromGff gffFile \n" " Create genePred objects from a GFF file..If -output is specified, the\n" " objects are written to that file.\n" "\n" "o fromGtf gtfFile \n" " Create genePred objects from a GTF file..If -output is specified, the\n" " objects are written to that file.\n" "\n" "Options:\n" " -verbose=1 - set verbose level\n" " -scoreFld - include id field\n" " -name2Fld - include name2 field\n" " -cdsStatFld - include cdsStat fields\n" " -exonFramesFld - include exonFrames field\n" " -genePredExt - include all extended fields\n" " -maxRows=n - maximum number of records to process\n" " -minRows=1 - error if less than this number of rows read\n" " -needRows=n - error if this number of rows read doesn't match\n" " -where=where - optional where clause for query\n" " -chrom=chrom - restrict file reading to this chromosome\n" " -output=fname - write output to this file \n" " -info=fname - write info about genePred to this file.\n" " -withBin - create bin column when loading a table\n" " -exonSelectWord=feat - use feat as the exon feature name when creating\n" " from GFF\n" " -ignoreUnconverted - don't print warnings when genens couldn't be converted\n" " to genePreds\n" " -impliedStopAfterCds - implied stop codon in GFF/GTF after CDS\n" " -noCheck - don't geneCheck results\n", msg); } static struct optionSpec options[] = { {"scoreFld", OPTION_BOOLEAN}, {"name2Fld", OPTION_BOOLEAN}, {"cdsStatFld", OPTION_BOOLEAN}, {"exonFramesFld", OPTION_BOOLEAN}, {"genePredExt", OPTION_BOOLEAN}, {"maxRows", OPTION_INT}, {"minRows", OPTION_INT}, {"needRows", OPTION_INT}, {"where", OPTION_STRING}, {"output", OPTION_STRING}, {"info", OPTION_STRING}, {"withBin", OPTION_BOOLEAN}, {"noCheck", OPTION_BOOLEAN}, {"exonSelectWord", OPTION_STRING}, {"ignoreUnconverted", OPTION_BOOLEAN}, {"impliedStopAfterCds", OPTION_BOOLEAN}, {NULL, 0}, }; unsigned gOptFields = genePredNoOptFld;; unsigned gCreateOpts = genePredBasicSql; unsigned gGxfCreateOpts = genePredGxfDefaults; int gMaxRows = BIGNUM; int gMinRows = 1; int gNeedRows = -1; char *gWhere = NULL; char *gChrom = NULL; char *gOutput = NULL; char *gInfo = NULL; char *gExonSelectWord = NULL; boolean gIgnoreUnconverted = FALSE; boolean gNoCheck = FALSE; int errCount = 0; void checkGenePred(char *desc, struct genePred* gp) /* check a genePred */ { if (!gNoCheck) { if (genePredCheck(desc, stderr, -1, gp) > 0) errCount++; } } void checkNumRows(char *src, int numRows) /* check the number of row constraints */ { if (numRows < gMinRows) errAbort("expected at least %d rows from %s, got %d", gMinRows, src, numRows); if ((gNeedRows >= 0) && (numRows != gNeedRows)) errAbort("expected %d rows from %s, got %d", gNeedRows, src, numRows); verbose(2, "read %d rows from %s\n", numRows, src); } void writeOptField(FILE* infoFh, struct genePred *gp, char* desc, enum genePredFields field) /* write info about one field */ { fprintf(infoFh, "%s: %s\n", desc, ((gp->optFields & field) ? "yes" : "no")); } void writeInfo(struct genePred *gp) /* write info about the genePred to the info file */ { if (gInfo != NULL) { FILE *infoFh = mustOpen(gInfo, "w"); writeOptField(infoFh, gp, "genePredScoreFld", genePredScoreFld); writeOptField(infoFh, gp, "genePredName2Fld", genePredName2Fld); writeOptField(infoFh, gp, "genePredCdsStatFld", genePredCdsStatFld); writeOptField(infoFh, gp, "genePredExonFramesFld", genePredExonFramesFld); carefulClose(&infoFh); } } void readTableTask(char *db, char *table) /* Implements the readTable task */ { FILE *outFh = NULL; struct sqlConnection *conn = sqlConnect(db); struct genePredReader* gpr = genePredReaderQuery(conn, table, gWhere); struct genePred* gp; int numRows = 0; if (gOutput != NULL) outFh = mustOpen(gOutput, "w"); while ((numRows < gMaxRows) && ((gp = genePredReaderNext(gpr)) != NULL)) { checkGenePred(table, gp); if (outFh != NULL) genePredTabOut(gp, outFh); if (numRows == 0) writeInfo(gp); genePredFree(&gp); numRows++; } carefulClose(&outFh); genePredReaderFree(&gpr); sqlDisconnect(&conn); checkNumRows(table, numRows); } void loadTableTask(char *db, char *table, char* gpFile) /* Implements the loadTable task */ { struct genePredReader* gpr = genePredReaderFile(gpFile, gChrom); char *sqlCmd = genePredGetCreateSql(table, gOptFields, gCreateOpts, 0); struct sqlConnection *conn; struct genePred* gp; int numRows = 0; char tabFile[PATH_LEN]; FILE *tabFh; safef(tabFile, sizeof(tabFile), "genePred.%d.tmp", getpid()); tabFh = mustOpen(tabFile, "w"); while ((numRows < gMaxRows) && ((gp = genePredReaderNext(gpr)) != NULL)) { if (gCreateOpts & genePredWithBin) fprintf(tabFh, "%u\t", binFromRange(gp->txStart, gp->txEnd)); checkGenePred(gpFile, gp); genePredTabOut(gp, tabFh); if (numRows == 0) writeInfo(gp); genePredFree(&gp); numRows++; } carefulClose(&tabFh); conn = sqlConnect(db); sqlRemakeTable(conn, table, sqlCmd); sqlLoadTabFile(conn, tabFile, table, 0); sqlDisconnect(&conn); unlink(tabFile); freeMem(sqlCmd); genePredReaderFree(&gpr); checkNumRows(gpFile, numRows); } void readFile(char *gpFile) /* Implements the readFile task */ { FILE *outFh = NULL; struct genePredReader* gpr = genePredReaderFile(gpFile, gChrom); struct genePred* gp; int numRows = 0; if (gOutput != NULL) outFh = mustOpen(gOutput, "w"); while ((numRows < gMaxRows) && ((gp = genePredReaderNext(gpr)) != NULL)) { checkGenePred(gpFile, gp); if (outFh != NULL) genePredTabOut(gp, outFh); if (numRows == 0) writeInfo(gp); genePredFree(&gp); numRows++; } carefulClose(&outFh); genePredReaderFree(&gpr); checkNumRows(gpFile, numRows); } struct hash* loadCds(char* cdsFile) /* load a CDS file into a hash */ { struct lineFile* lf = lineFileOpen(cdsFile, TRUE); struct hash* cdsTbl = hashNew(0); char *row[2]; while (lineFileNextRowTab(lf, row, 2)) { struct genbankCds* cds; lmAllocVar(cdsTbl->lm, cds); if (!genbankCdsParse(row[1], cds)) errAbort("invalid CDS for %s: %s", row[0], row[1]); hashAdd(cdsTbl, row[0], cds); } lineFileClose(&lf); return cdsTbl; } void fromPsl(char *pslFile, char* cdsFile) /* Implements the fromPsl task */ { struct psl* pslList = pslLoadAll(pslFile); struct hash *cdsTbl = loadCds(cdsFile); struct psl *psl; FILE *outFh = NULL; int numRows = 0; if (gOutput != NULL) outFh = mustOpen(gOutput, "w"); for (psl = pslList; (psl != NULL) && (numRows < gMaxRows); psl = psl->next, numRows++) { struct genbankCds* cds = hashFindVal(cdsTbl, psl->qName); struct genePred* gp = genePredFromPsl2(psl, gOptFields, cds, 5); checkGenePred(pslFile, gp); if (outFh != NULL) genePredTabOut(gp, outFh); if (numRows == 0) writeInfo(gp); genePredFree(&gp); } pslFreeList(&pslList); carefulClose(&outFh); hashFree(&cdsTbl); checkNumRows(pslFile, numRows); } void groupConvertWarn(char *gxfFile, boolean isGtf, struct gffGroup *group) /* issue a warning when a GxF group can't be converted to a genePred */ { struct gffLine *line; fprintf(stderr, "Warning: Can't convert %s to genePred: %s\n", (isGtf ? "GTF" : "GFF"), gxfFile); for (line = group->lineList; line != NULL; line = line->next) { - fprintf(stderr, "\t%s\t%s\t%s\t%d\t%d\t%g\t%c\t%c\t%s\t%s\t%s\t%d\n", + fprintf(stderr, "\t%s\t%s\t%s\t%ld\t%ld\t%g\t%c\t%c\t%s\t%s\t%s\t%d\n", line->seq, line->source, line->feature, line->start, line->end, line->score, line->strand, line->frame, line->group, line->geneId, line->exonId, line->exonNumber); } } void fromGxf(char *gxfFile, boolean isGtf) /* Implements the fromGff/fromGtf tasks */ { struct gffFile *gxf = gffRead(gxfFile); struct gffGroup *group; struct genePred *gp; int numRows = 0; FILE *outFh = NULL; if (gOutput != NULL) outFh = mustOpen(gOutput, "w"); gffGroupLines(gxf); for (group = gxf->groupList; group != NULL; group = group->next) { if (isGtf) gp = genePredFromGroupedGtf(gxf, group, group->name, gOptFields, gGxfCreateOpts); else gp = genePredFromGroupedGff(gxf, group, group->name, gExonSelectWord, gOptFields, gGxfCreateOpts); if (gp == NULL) { if (!gIgnoreUnconverted) groupConvertWarn(gxfFile, isGtf, group); } else { checkGenePred(gxfFile, gp); if (outFh != NULL) genePredTabOut(gp, outFh); if (numRows == 0) writeInfo(gp); genePredFree(&gp); numRows++; } } gffFileFree(&gxf); carefulClose(&outFh); } int main(int argc, char *argv[]) /* Process command line. */ { char *task; optionInit(&argc, argv, options); if (argc < 2) usage("must supply a task"); task = argv[1]; if (optionExists("scoreFld")) gOptFields |= genePredScoreFld; if (optionExists("name2Fld")) gOptFields |= genePredName2Fld; if (optionExists("cdsStatFld")) gOptFields |= genePredCdsStatFld; if (optionExists("exonFramesFld")) gOptFields |= genePredExonFramesFld; if (optionExists("genePredExt")) gOptFields |= genePredAllFlds; gMaxRows = optionInt("maxRows", gMaxRows); gMinRows = optionInt("minRows", gMinRows); gNeedRows = optionInt("minRows", gNeedRows); gWhere = optionVal("where", gWhere); gChrom = optionVal("chrom", gChrom); gOutput = optionVal("output", gOutput); gInfo = optionVal("info", gInfo); gNoCheck = optionExists("noCheck"); gExonSelectWord = optionVal("exonSelectWord", gExonSelectWord); gIgnoreUnconverted = optionExists("ignoreUnconverted"); if (optionExists("impliedStopAfterCds")) gGxfCreateOpts |= genePredGxfImpliedStopAfterCds; if (optionExists("withBin")) gCreateOpts |= genePredWithBin; if (sameString(task, "readTable")) { if (argc != 4) usage("readTable task requires two arguments"); readTableTask(argv[2], argv[3]); } else if (sameString(task, "loadTable")) { if (argc != 5) usage("loadTable task requires three arguments"); loadTableTask(argv[2], argv[3], argv[4]); } else if (sameString(task, "readFile")) { if (argc != 3) usage("readFile task requires one argument"); readFile(argv[2]); } else if (sameString(task, "fromPsl")) { if (argc != 4) usage("fromPsl task requires two argument"); fromPsl(argv[2], argv[3]); } else if (sameString(task, "fromGff")) { if (argc != 3) usage("fromGff task requires one argument"); fromGxf(argv[2], FALSE); } else if (sameString(task, "fromGtf")) { if (argc != 3) usage("fromGtf task requires one argument"); fromGxf(argv[2], TRUE); } else { usage("invalid task"); } return (errCount == 0) ? 0 : 1; }