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/ratStuff/mafGene/mafGene.c src/hg/ratStuff/mafGene/mafGene.c index 2a78da2..4407174 100644 --- src/hg/ratStuff/mafGene/mafGene.c +++ src/hg/ratStuff/mafGene/mafGene.c @@ -1,287 +1,287 @@ /* mafGene - output protein alignments using maf and frames. */ /* Copyright (C) 2013 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 "linefile.h" #include "hash.h" #include "options.h" #include "hdb.h" #include "maf.h" #include "obscure.h" #include "genePred.h" #include "mafGene.h" #include "genePredReader.h" void usage() /* Explain usage and exit. */ { errAbort( "mafGene - output protein alignments using maf and genePred\n" "usage:\n" " mafGene dbName mafTable genePredTable species.lst output\n" "arguments:\n" " dbName name of SQL database\n" " mafTable name of maf file table\n" " genePredTable name of the genePred table\n" " species.lst list of species names\n" " output put output here\n" "options:\n" " -useFile genePredTable argument is a genePred file name\n" " -geneName=foobar name of gene as it appears in genePred\n" " -geneList=foolst name of file with list of genes\n" " -geneBeds=foo.bed name of bed file with genes and positions\n" " -chrom=chr1 name of chromosome from which to grab genes\n" " -exons output exons\n" " -noTrans don't translate output into amino acids\n" " -uniqAA put out unique pseudo-AA for every different codon\n" " -includeUtr include the UTRs, use only with -noTrans\n" " -delay=N delay N seconds between genes (default 0)\n" " -noDash don't output lines with all dashes\n" ); } static struct optionSpec options[] = { {"geneName", OPTION_STRING}, {"geneList", OPTION_STRING}, {"geneBeds", OPTION_STRING}, {"chrom", OPTION_STRING}, {"exons", OPTION_BOOLEAN}, {"noTrans", OPTION_BOOLEAN}, {"noDash", OPTION_BOOLEAN}, {"uniqAA", OPTION_BOOLEAN}, {"useFile", OPTION_BOOLEAN}, {"includeUtr", OPTION_BOOLEAN}, {"delay", OPTION_INT}, {NULL, 0}, }; char *geneName = NULL; char *geneList = NULL; char *geneBeds = NULL; char *onlyChrom = NULL; boolean inExons = FALSE; boolean noTrans = TRUE; int delay = 0; boolean newTableType; boolean uniqAA = FALSE; boolean noDash = FALSE; boolean useFile = FALSE; boolean includeUtr = FALSE; /* load one or more genePreds from the database */ struct genePred *getPredsForName(char *name, char *geneTable, char *db) { struct sqlConnection *conn = hAllocConn(db); struct genePred *list = NULL; char splitTable[HDB_MAX_TABLE_STRING]; struct genePred *gene; struct genePredReader *reader; boolean found = hFindSplitTable(db, NULL, geneTable, splitTable, sizeof splitTable, NULL); if (!found) errAbort("can't find table %s\n", geneTable); char extra[2048]; if (onlyChrom != NULL) safef(extra, sizeof extra, "name='%s' and chrom='%s'", name, onlyChrom); else safef(extra, sizeof extra, "name='%s'", name); reader = genePredReaderQuery( conn, splitTable, extra); while ((gene = genePredReaderNext(reader)) != NULL) { verbose(2, "got gene %s\n",gene->name); slAddHead(&list, gene); } if (list == NULL) errAbort("no genePred for gene %s in %s\n",name, geneTable); slReverse(&list); genePredReaderFree(&reader); hFreeConn(&conn); return list; } /* output the sequence for one gene for every species to * the file stream */ void outGenePred(FILE *f, struct genePred *pred, char *dbName, char *mafTable, char *geneTable, struct slName *speciesNameList) { unsigned options = 0; if (uniqAA) options |= MAFGENE_UNIQUEAA; if (inExons) options |= MAFGENE_EXONS; if (noTrans) options |= MAFGENE_NOTRANS; if (!noDash) options |= MAFGENE_OUTBLANK; if (includeUtr) options |= MAFGENE_INCLUDEUTR; mafGeneOutPred(f, pred, dbName, mafTable, speciesNameList, options, 0); } /* read a list of single words from a file */ static struct slName *readList(char *fileName) { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct slName *list = NULL; char *row[1]; while (lineFileRow(lf, row)) { int len = strlen(row[0]); struct slName *sn = needMem(sizeof(*sn)+len); strcpy(sn->name, row[0]); slAddHead(&list, sn); } slReverse(&list); lineFileClose(&lf); return list; } /* query the list of gene names from the frames table */ static struct genePred *queryPreds(char *dbName, char *geneTable) { struct sqlConnection *conn = hAllocConn(dbName); struct genePred *list = NULL; char buf[2048]; char *extra = NULL; struct genePredReader *reader; if (onlyChrom != NULL) { safef(buf, sizeof buf, "chrom='%s'", onlyChrom); extra = buf; } reader = genePredReaderQuery( conn, geneTable, extra); list = genePredReaderAll(reader); hFreeConn(&conn); return list; } struct genePred *getPredsFromBeds(char *file, char *table, char *db) { struct sqlConnection *conn = hAllocConn(db); struct lineFile *lf = lineFileOpen(file, TRUE); char *words[5000]; int wordsRead; struct genePred *list = NULL; while( (wordsRead = lineFileChopNext(lf, words, sizeof(words)/sizeof(char *)) )) { if (wordsRead != 4) errAbort("file '%s' must be bed4. Line %d has %d fields", file, lf->lineIx, wordsRead); char where[10 * 1024]; sqlSafefFrag(where, sizeof where, "name = '%s' and chrom='%s' and txStart = %d and txEnd = %d", words[3], words[0], sqlUnsigned(words[1]), sqlUnsigned(words[2])); //printf("table %s where %s\n",table,where); struct genePredReader *reader = genePredReaderQuery( conn, table, where); struct genePred *pred; while ((pred = genePredReaderNext(reader)) != NULL) slAddHead(&list, pred); genePredReaderFree(&reader); } hFreeConn(&conn); if (list != NULL) slReverse(&list); return list; } void mafGene(char *dbName, char *mafTable, char *geneTable, char *speciesList, char *outName) /* mafGene - output protein alignments using maf and genePred. */ { struct slName *speciesNames = readList(speciesList); FILE *f = mustOpen(outName, "w"); struct genePred *list = NULL; if (geneList != NULL) { struct slName *geneNames = readList(geneList); for(; geneNames; geneNames = geneNames->next) { struct genePred *pred = getPredsForName(geneNames->name, geneTable, dbName); if (pred != NULL) slCat(&list, pred); } } else if (useFile) /* Read genePreds from a file passed instead of a table */ list = genePredReaderLoadFile(geneTable, NULL); else if (geneName != NULL) list = getPredsForName(geneName, geneTable, dbName); else if (geneBeds != NULL) list = getPredsFromBeds(geneBeds, geneTable, dbName); else list = queryPreds(dbName, geneTable); for(; list; list = list->next) { verbose(2, "outting gene %s \n",list->name); outGenePred(f, list, dbName, mafTable, geneTable, speciesNames); if (delay) { verbose(2, "delaying %d seconds\n",delay); sleep(delay); } } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 6) usage(); geneName = optionVal("geneName", geneName); geneList = optionVal("geneList", geneList); geneBeds = optionVal("geneBeds", geneBeds); onlyChrom = optionVal("chrom", onlyChrom); inExons = optionExists("exons"); uniqAA = optionExists("uniqAA"); noDash = optionExists("noDash"); noTrans = optionExists("noTrans"); includeUtr = optionExists("includeUtr"); useFile = optionExists("useFile"); delay = optionInt("delay", delay); if (((geneName != NULL) && ((geneList != NULL) || geneBeds != NULL)) || ((geneList != NULL) && ((geneName != NULL) || geneBeds != NULL)) || ((geneBeds != NULL) && ((geneList != NULL) || geneName != NULL))) errAbort("must specify only one of geneList, geneName, geneBeds"); if ((geneBeds != NULL) && (onlyChrom != NULL)) errAbort("cannot specify beds and chrom"); if (includeUtr && !noTrans) errAbort("must specify noTrans if includeUtr is selected"); mafGene(argv[1],argv[2],argv[3],argv[4],argv[5]); return 0; }