e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/hgGene/rgdInfo.c src/hg/hgGene/rgdInfo.c index 96f1892..279a082 100644 --- src/hg/hgGene/rgdInfo.c +++ src/hg/hgGene/rgdInfo.c @@ -1,332 +1,335 @@ /* rgdGeneInfo - functions related to RGD Genes */ +/* Copyright (C) 2013 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #include "common.h" #include "hash.h" #include "linefile.h" #include "dystring.h" #include "hdb.h" #include "hgGene.h" // define external URLs used #define RGD_GENE_URL "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" #define PUBMED_URL "http://www.ncbi.nlm.nih.gov/pubmed/" #define GBNK_PROT_URL "http://www.ncbi.nlm.nih.gov/protein/" #define GBNK_DNA_URL "http://www.ncbi.nlm.nih.gov/nuccore/" #define ENTREZ_URL "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=retrieve&list_uids=" #define UNIPROT_URL "http://www.uniprot.org/uniprot/" #define UNIGENE_URL "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Rn&CID=" #define ENSEMBL_URL "http://www.ensembl.org/Rattus_norvegicus/Gene/Summary?g=" #define TIGR_URL "http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_report.pl?gudb=rat&tc=" #define SSLP_URL "http://rgd.mcw.edu/objectSearch/sslpReport.jsp?rgd_id=" #define QTL_URL "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=" #define IMAGE_URL "http://image.hudsonalpha.org/IQ/bin/singleCloneQuery?clone_id=" #define MGC_URL "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Rn&LIST=" char *getRgdGeneId(struct sqlConnection *conn, char *geneId) /* Return rgdGene ID for now. */ { return(geneId); } char *getRgdGeneUniProtAcc(char *geneId, struct sqlConnection *conn) /* get UniProt Acc from an RGD Gene ID */ { char query[256]; struct sqlResult *sr; char **row; char *protAcc; sqlSafef(query, sizeof(query), "select value from rgdGene2ToUniProt where name = '%s'", geneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { protAcc = strdup(row[0]); sqlFreeResult(&sr); return(protAcc); } else { sqlFreeResult(&sr); return(NULL); } } boolean isRgdGene(struct sqlConnection *conn) /* Return true if the gene set is RGD Genes. */ { /* The existence of the table rgdGene2Raw storing * GENES_RAT data from RGD indicates that we are using RGD Genes as * our main gene set for this genome. */ return(hTableExists(sqlGetDatabase(conn), "rgdGene2Raw")); } static boolean rgdGeneInfoExists(struct section *section, struct sqlConnection *conn, char *geneId) /* Return TRUE if rgdGene info tables exist. */ { char *rgdGeneId = getRgdGeneId(conn, geneId); if (rgdGeneId == NULL) return FALSE; else return(TRUE); } void do1Colx(char **row, int iCol, char *colName, char *entryName, char *externalUrl) { char *chp, *chp1; if (strlen(row[iCol]) > 0) { printf("<b>%s:</b>\n", entryName); if (externalUrl == NULL) { printf("%s<br>", row[iCol]); return; } chp1 = row[iCol]; chp = chp1; chp++; while (*chp != '\0') { if (*chp == ',') { *chp = '\0'; printf("<A HREF=\"%s", externalUrl); printf("%s", chp1);fflush(stdout); printf("\" TARGET=_blank>%s</A>, ", chp1);fflush(stdout); chp1 = chp; chp1++; } chp ++; } /* print the last entry */ printf("<A HREF=\"%s", externalUrl); printf("%s", chp1); printf("\" TARGET=_blank>%s</A>", chp1); printf("<br>\n"); } } void do1Col(char **row, int iCol, char *colName) { if (strlen(row[iCol]) > 0) { printf("<b>%s:</b> %s<br>\n", colName, row[iCol]);fflush(stdout); } } static void rgdGeneInfoPrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print out RgdGene info. */ { char *rgdGeneId = getRgdGeneId(conn, geneId); char query[256], **row; struct sqlResult *sr; char *chp; int iCol; chp = strstr(rgdGeneId, ":"); chp++; sqlSafef(query, sizeof(query), "select * from %s where gene_rgd_id='%s'", section->rgdGeneTable, chp); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { /* Data of some columns are not displayed. The statements for those are left there but commented out for documentation purpose. In case we need additional variables displayed, just un-comment the lines. */ iCol = 0; do1Colx(row, iCol, "gene_rgd_id", "RGD Gene", RGD_GENE_URL); iCol++; do1Colx(row, iCol, "symbol", "Gene Symbol", NULL); iCol++; do1Colx(row, iCol, "name", "Name", NULL); iCol++; //do1Col(row, iCol, "gene_desc"); iCol++; //do1Col(row, iCol, "chromosome_celera"); iCol++; //do1Col(row, iCol, "chromosome_31"); iCol++; //do1Col(row, iCol, "chromosome_34"); iCol++; //do1Col(row, iCol, "fish_band"); iCol++; //do1Col(row, iCol, "start_pos_celera"); iCol++; //do1Col(row, iCol, "stop_pos_celera"); iCol++; //do1Col(row, iCol, "strand_celera"); iCol++; //do1Col(row, iCol, "start_pos_31"); iCol++; //do1Col(row, iCol, "stop_pos_31"); iCol++; //do1Col(row, iCol, "strand_31"); iCol++; //do1Col(row, iCol, "start_pos_34"); iCol++; //do1Col(row, iCol, "stop_pos_34"); iCol++; //do1Col(row, iCol, "strand_34"); iCol++; //do1Col(row, iCol, "curated_ref_rgd_id"); iCol++; do1Colx(row, iCol, "curated_ref_pubmed_id", "Curated Pubmed Papers", PUBMED_URL); iCol++; do1Colx(row, iCol, "uncurated_pubmed_id", "Uncurated Pubmed Papers", PUBMED_URL); iCol++; //do1Col(row, iCol, "ratmap_id"); iCol++; do1Colx(row, iCol, "entrez_gene", "Entrez Gene", ENTREZ_URL); iCol++; do1Colx(row, iCol, "uniprot_id", "UniProt", UNIPROT_URL); iCol++; //do1Col(row, iCol, "rhdb_id"); iCol++; //do1Col(row, iCol, "uncurated_ref_medline_id"); iCol++; do1Colx(row, iCol, "genbank_nucleotide", "GenBank Nucleotide", GBNK_DNA_URL); iCol++; do1Colx(row, iCol, "tigr_id", "TIGR", TIGR_URL); iCol++; do1Colx(row, iCol, "genbank_protein", "Genebank Protein", GBNK_PROT_URL); iCol++; stripString(row[iCol],"Rn."); do1Colx(row, iCol, "unigene_id", "UniGene", UNIGENE_URL); iCol++; //do1Col(row, iCol, "gdb_id"); iCol++; do1Colx(row, iCol, "sslp_rgd_id", "RGD SSLP", SSLP_URL); iCol++; //do1Col(row, iCol, "sslp_symbol"); iCol++; //do1Col(row, iCol, "old_symbol"); iCol++; //do1Col(row, iCol, "old_name"); iCol++; do1Colx(row, iCol, "qtl_rgd_id", "RGD QTL", QTL_URL); iCol++; //do1Col(row, iCol, "qtl_symbol"); iCol++; //do1Col(row, iCol, "nomenclature_status"); iCol++; //do1Col(row, iCol, "splice_rgd_id"); iCol++; //do1Col(row, iCol, "splice_symbol"); iCol++; //do1Col(row, iCol, "gene_type"); iCol++; do1Colx(row, iCol, "ensembl_id", "Ensembl Gene", ENSEMBL_URL); } sqlFreeResult(&sr); /* display IMAGE info */ sqlSafef(query, sizeof(query), "select info from rgdGene2Xref where rgdGeneId='%s' and infoType='IMAGE'", rgdGeneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<b>IMAGE CLONE: </b>"); while (row != NULL) { printf("<A HREF=\"%s", IMAGE_URL); printf("%s", row[0]);fflush(stdout); printf("\" TARGET=_blank>%s</A>", row[0]);fflush(stdout); row = sqlNextRow(sr); if (row != NULL) printf(", "); } printf("<br>"); } sqlFreeResult(&sr); /* display MGC info */ sqlSafef(query, sizeof(query), "select info from rgdGene2Xref where rgdGeneId='%s' and infoType='MGC'", rgdGeneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("<b>MGC: </b>"); while (row != NULL) { printf("<A HREF=\"%s", MGC_URL); printf("%s", row[0]);fflush(stdout); printf("\" TARGET=_blank>%s</A>", row[0]);fflush(stdout); row = sqlNextRow(sr); if (row != NULL) printf(", "); } printf("<br>"); } sqlFreeResult(&sr); } struct section *rgdGeneInfoSection(struct sqlConnection *conn, struct hash *sectionRa, char *sectionName, char *table) /* Create RgdGene info section. */ { struct section *section = sectionNew(sectionRa, sectionName); if (section != NULL) { section->exists = rgdGeneInfoExists; section->print = rgdGeneInfoPrint; section->rgdGeneTable = table; } return section; } /* display info from downloaded raw data file */ struct section *rgdGeneRawSection(struct sqlConnection *conn, struct hash *sectionRa) /* Create RgdGene roles section. */ { return rgdGeneInfoSection(conn, sectionRa, "rgdGeneRaw", "rgdGene2Raw"); }