4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/makeDb/ldHgGene/ldHgGene.c src/hg/makeDb/ldHgGene/ldHgGene.c index ac14f16..1b7c7ad 100644 --- src/hg/makeDb/ldHgGene/ldHgGene.c +++ src/hg/makeDb/ldHgGene/ldHgGene.c @@ -1,227 +1,227 @@ /* ldHgGene - load a set of gene predictions from GFF or GTF file into * mySQL database. */ /* Copyright (C) 2011 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "options.h" #include "hash.h" #include "dystring.h" #include "linefile.h" #include "hdb.h" #include "gff.h" #include "jksql.h" #include "genePred.h" #include "hgRelate.h" char *exonType = "exon"; /* Type field that signifies exons. */ boolean requireCDS = FALSE; /* should genes with CDS be dropped */ boolean useBin = TRUE; /* add bin column */ char *outFile = NULL; /* Output file as alternative to database. */ unsigned gOptFields = 0; /* optional fields from cmdline */ unsigned gCreateOpts = 0; /* table create options from cmdline */ unsigned gGxfOptions = 0; /* options for converting GTF/GFF */ /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"exon", OPTION_STRING}, {"oldTable", OPTION_BOOLEAN}, {"noncoding", OPTION_BOOLEAN}, {"nonCoding", OPTION_BOOLEAN}, {"gtf", OPTION_BOOLEAN}, {"bin", OPTION_BOOLEAN}, {"nobin", OPTION_BOOLEAN}, {"predTab", OPTION_BOOLEAN}, {"requireCDS", OPTION_BOOLEAN}, {"genePredExt", OPTION_BOOLEAN}, {"impliedStopAfterCds", OPTION_BOOLEAN}, {"out", OPTION_STRING}, {NULL, 0} }; void usage() { errAbort( "ldHgGene - load database with gene predictions from a gff file.\n" "usage:\n" " ldHgGene database table file(s).gff\n" "options:\n" " -bin Add bin column (now the default)\n" " -nobin don't add binning (you probably don't want this)\n" " -exon=type Sets type field for exons to specific value\n" " -oldTable Don't overwrite what's already in table\n" " -noncoding Forces whole prediction to be UTR\n" " -gtf input is GTF, stop codon is not in CDS\n" " -predTab input is already in genePredTab format\n" " -requireCDS discard genes that don't have CDS annotation\n" " -out=gpfile write output, in genePred format, instead of loading\n" " table. Database is ignored.\n" " -genePredExt create a extended genePred, including frame\n" " information and gene name\n" " -impliedStopAfterCds - implied stop codon in GFF/GTF after CDS\n"); } void loadIntoDatabase(char *database, char *table, char *tabName, bool appendTbl) /* Load tabbed file into database table. Drop and create table. */ { struct sqlConnection *conn = sqlConnect(database); if (!appendTbl) { char *createSql = genePredGetCreateSql(table, gOptFields, gCreateOpts, hGetMinIndexLength(database)); sqlRemakeTable(conn, table, createSql); freeMem(createSql); } sqlLoadTabFile(conn, tabName, table, SQL_TAB_FILE_WARN_ON_WARN); /* add a comment to the history table and finish up connection */ hgHistoryComment(conn, "Add gene predictions to %s table %s frame info.", table, ((gOptFields & genePredExonFramesFld) ? "with" : "w/o")); sqlDisconnect(&conn); } char *convertSoftberryName(char *name) /* Convert softberry name to simple form that is same as in * softberryPep table. */ { static char *head = "gene_id S."; char *s = strrchr(name, '.'); if (strstr(name, head) == NULL) errAbort("Unrecognized Softberry name %s, no %s", name, head); return s+1; } void ldHgGenePred(char *database, char *table, int gCount, char *gNames[]) /* Load up database from a bunch of genePred files. */ { char *tabName = "genePred.tab"; FILE *f; struct genePred *gpList = NULL, *gp; int i; for (i=0; i<gCount; ++i) { verbose(1, "Reading %s\n", gNames[i]); gpList = slCat(genePredExtLoadAll(gNames[i]), gpList); } verbose(1, "%d gene predictions\n", slCount(gpList)); slSort(&gpList, genePredCmp); /* Create tab-delimited file. */ if (outFile != NULL) f = mustOpen(outFile, "w"); else f = mustOpen(tabName, "w"); for (gp = gpList; gp != NULL; gp = gp->next) { if (useBin) fprintf(f, "%d\t", hFindBin(gp->txStart, gp->txEnd)); genePredTabOut(gp, f); } carefulClose(&f); if (outFile == NULL) loadIntoDatabase(database, table, tabName, optionExists("oldTable")); } void ldHgGene(char *database, char *table, int gtfCount, char *gtfNames[]) /* Load up database from a bunch of GTF files. */ { struct gffFile *gff = gffFileNew(""); struct gffGroup *group; int i; int lineCount; struct genePred *gpList = NULL, *gp; char *tabName = "genePred.tab"; FILE *f; boolean nonCoding = optionExists("noncoding") || optionExists("nonCoding"); boolean isGtf = optionExists("gtf"); boolean isSoftberry = sameWord("softberryGene", table); for (i=0; i<gtfCount; ++i) { verbose(1, "Reading %s\n", gtfNames[i]); gffFileAdd(gff, gtfNames[i], 0); } lineCount = slCount(gff->lineList); verbose(1, "Read %d transcripts in %d lines in %d files\n", slCount(gff->groupList), lineCount, gtfCount); gffGroupLines(gff); verbose(1, " %d groups %d seqs %d sources %d feature types\n", slCount(gff->groupList), slCount(gff->seqList), slCount(gff->sourceList), slCount(gff->featureList)); /* Convert from gffGroup to genePred representation. */ for (group = gff->groupList; group != NULL; group = group->next) { char *name = group->name; if (isSoftberry) { name = convertSoftberryName(name); } if (isGtf) gp = genePredFromGroupedGtf(gff, group, name, gOptFields, gGxfOptions); else gp = genePredFromGroupedGff(gff, group, name, exonType, gOptFields, gGxfOptions); if (gp != NULL) { if (nonCoding) gp->cdsStart = gp->cdsEnd = 0; if (requireCDS && (gp->cdsStart == gp->cdsEnd)) genePredFree(&gp); else slAddHead(&gpList, gp); } } verbose(1, "%d gene predictions\n", slCount(gpList)); slSort(&gpList, genePredCmp); /* Create tab-delimited file. */ if (outFile != NULL) f = mustOpen(outFile, "w"); else f = mustOpen(tabName, "w"); for (gp = gpList; gp != NULL; gp = gp->next) { if (useBin) fprintf(f, "%d\t", hFindBin(gp->txStart, gp->txEnd)); genePredTabOut(gp, f); } carefulClose(&f); if (outFile == NULL) loadIntoDatabase(database, table, tabName, optionExists("oldTable")); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc < 3) usage(); if (optionExists("exon") && optionExists("gtf")) errAbort("can't specify -exon= with -gtf"); exonType = optionVal("exon", exonType); outFile = optionVal("out", NULL); requireCDS = optionExists("requireCDS"); if (optionExists("bin") && optionExists("nobin")) errAbort("can't specify both -bin and -nobin"); useBin = !optionExists("nobin"); if (optionExists("genePredExt")) gOptFields |= genePredAllFlds; if (useBin) gCreateOpts |= genePredWithBin; if (optionExists("impliedStopAfterCds")) gGxfOptions |= genePredGxfImpliedStopAfterCds; if (optionExists("predTab")) ldHgGenePred(argv[1], argv[2], argc-3, argv+3); else ldHgGene(argv[1], argv[2], argc-3, argv+3); return 0; }