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/protein/kgBioCyc1/kgBioCyc1.c src/hg/protein/kgBioCyc1/kgBioCyc1.c index 8547204..853c53e 100644 --- src/hg/protein/kgBioCyc1/kgBioCyc1.c +++ src/hg/protein/kgBioCyc1/kgBioCyc1.c @@ -1,215 +1,215 @@ /* kgBioCyc1 - Create tab separated files for bioCyc tables.. */ /* Copyright (C) 2014 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 "jksql.h" #include "options.h" #include "obscure.h" void usage() /* Explain usage and exit. */ { errAbort( "kgBioCyc1 - Create tab separated files for bioCyc tables.\n" "usage:\n" " kgBioCyc1 genes.tab pathways.tab database bioCycPathway.tab bioCycMapDesc.tab\n" "options:\n" " -noEnsembl don't use Ensembl tables to look up id\n" ); } static struct optionSpec options[] = { {"noEnsembl", OPTION_BOOLEAN}, {NULL, 0}, }; boolean noEnsembl = FALSE; void checkWordMatch(char *fileName, char **words, int lineIx, int wordIx, char *expecting) /* CHeck that words[wordIx] is same as expecting or report error and abort. */ { if (!sameWord(words[wordIx], expecting)) errAbort("Expecting %s, got %s, line %d word %d of %s", expecting, words[wordIx], lineIx+1, wordIx+1, fileName); } struct hash *hashBioCycGenes(char *geneFile, char *db) /* Build up a hash of bioCycGenes keyed by bioCyc gene name and with ucscGene values. */ { /* Open up file, read first line, and chop it into tab separated words. */ struct lineFile *lf = lineFileOpen(geneFile, TRUE); char *words[256]; int firstWordCount = lineFileChopNextTab(lf, words, ArraySize(words)); struct sqlConnection *conn = sqlConnect(db); char query[1024]; struct hash *hash = hashNew(16); /* Verify that the first fields of the first line are what we think. THese are the * labels for the table. */ if (firstWordCount < 9) errAbort("Not enough fields in %s\n", geneFile); checkWordMatch(geneFile, words, 0, 0, "UNIQUE-ID"); checkWordMatch(geneFile, words, 0, 1, "NAME"); checkWordMatch(geneFile, words, 0, 2, "PRODUCT-NAME"); checkWordMatch(geneFile, words, 0, 3, "SWISS-PROT-ID"); checkWordMatch(geneFile, words, 0, 4, "REPLICON"); checkWordMatch(geneFile, words, 0, 5, "START-BASE"); checkWordMatch(geneFile, words, 0, 6, "END-BASE"); /* Loop through each gene, trying to find a UCSC gene that fits. */ int wordCount; while ((wordCount = lineFileChopNextTab(lf, words, ArraySize(words))) > 0) { lineFileExpectWords(lf, firstWordCount, wordCount); char *bioCycId = words[0]; char *symbol = words[1]; char *knownGeneId = NULL; if (!noEnsembl) { /* BioCycId is really an ENSEMBL Gene ID. Use following SQL to look it up. */ sqlSafef(query, sizeof(query), "select distinct(knownCanonical.transcript) " "from ensGtp,knownToEnsembl,knownIsoforms,knownCanonical " "where ensGtp.gene = '%s' " "and ensGtp.transcript = knownToEnsembl.value " "and knownToEnsembl.name=knownIsoforms.transcript " "and knownCanonical.clusterId = knownIsoforms.clusterId", bioCycId); knownGeneId = sqlQuickString(conn, query); } /* If we don't have it, make an attempt to get it from gene symbol instead. */ if (knownGeneId == NULL) { char *escSym = makeEscapedString(symbol, '\''); sqlSafef(query, sizeof(query), "select distinct(knownCanonical.transcript) " "from kgXref,knownIsoforms,knownCanonical " "where kgXref.geneSymbol = '%s' " "and kgXref.kgID=knownIsoforms.transcript " "and knownIsoforms.clusterId = knownCanonical.clusterId", escSym); knownGeneId = sqlQuickString(conn, query); freeMem(escSym); } if (knownGeneId != NULL) hashAdd(hash, bioCycId, knownGeneId); } sqlDisconnect(&conn); return hash; } boolean allBlank(char **words, int start, int end) /* Return true if all words from start to end are empty. */ { int i; for (i=start; i<end; ++i) if (!isEmpty(words[i])) return FALSE; return TRUE; } void kgBioCyc1(char *inGenes, char *inPathways, char *inDatabase, char *outPathway, char *outDesc) /* kgBioCyc1 - Create tab separated files for bioCyc tables.. */ { struct hash *hash = hashBioCycGenes(inGenes, inDatabase); uglyf("Got %d elements in %s\n", hash->elCount, inGenes); /* Open, read in first line of pathways file (which contains column labels) * and sanity check it. */ struct lineFile *lf = lineFileOpen(inPathways, TRUE); char *words[64*1024]; int firstWordCount = lineFileChopNextTab(lf, words, ArraySize(words)); if (firstWordCount < 3) errAbort("Not enough fields in %s\n", inPathways); checkWordMatch(inPathways, words, 0, 0, "UNIQUE-ID"); checkWordMatch(inPathways, words, 0, 1, "NAME"); /* Figure out the first and last columns that have GENE-ID */ int firstGeneId = 0, lastGeneId = 0; int i; for (i=2; i<firstWordCount; ++i) { if (sameWord("GENE-ID", words[i])) { if (firstGeneId == 0) { firstGeneId = i; lastGeneId = i; } else { if (lastGeneId != i-1) errAbort("Expecting GENE-ID to be all together in line 1 of %s", inPathways); lastGeneId = i; } } } if (firstGeneId == 0) errAbort("Found no GENE-ID in first line of %s", inPathways); /* Open output files. */ FILE *fDesc = mustOpen(outDesc, "w"); FILE *fPathway = mustOpen(outPathway, "w"); /* GEt a database connection. */ struct sqlConnection *conn = sqlConnect(inDatabase); char query[512]; /* Loop through remaining lines, one for each pathway. */ int wordCount; while ((wordCount = lineFileChopNextTab(lf, words, ArraySize(words))) > 0) { char *pathwayId = words[0]; char *description = words[1]; fprintf(fDesc, "%s\t%s\n", pathwayId, description); /* Do a little error checking, and then write out pathway/description file. */ if (firstWordCount != wordCount) { /* The lines with no genes in the pathway seem to be missing some tabs.... */ if (!allBlank(words, 2, wordCount)) errAbort("Expecting %d words got %d line %d of %s.", firstWordCount, wordCount, lf->lineIx, lf->fileName); continue; } /* Write out a line in pathway file for each non-empty gene-id */ int i; for (i=firstGeneId; i <= lastGeneId; ++i) { char *gene = words[i]; if (!isEmpty(gene)) { char *ucscId = hashFindVal(hash, gene); if (ucscId != NULL) { sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgID = '%s'", ucscId); char *geneSymbol = sqlQuickString(conn, query); fprintf(fPathway, "%s\t%s\t%s\n", ucscId, geneSymbol, pathwayId); freeMem(geneSymbol); } } } } /* Clean up. */ carefulClose(&fDesc); carefulClose(&fPathway); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 6) usage(); noEnsembl = optionExists("noEnsembl"); kgBioCyc1(argv[1], argv[2], argv[3], argv[4], argv[5]); return 0; }