71c6d9c65dcbb95c4c1840a2409e7457aed62c66 markd Wed Jul 17 19:21:15 2019 -0700 removed links to HAVANA as database is archives and HAVANA ids are on their way out diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c index 95561c0..953ccc9 100644 --- src/hg/hgc/gencodeClick.c +++ src/hg/hgc/gencodeClick.c @@ -37,33 +37,30 @@ /* Various URLs and URL templates. At one time, these were in the ra file, * but that didn't prove that helpful and end up requiring updated the ra * files for every GENCODE version if a URL was added or changed. */ //FIXME: clean up RA files when CGIs no longer need them static char *ensemblTranscriptIdUrl = "http://www.ensembl.org/%s/Transcript/Summary?db=core;t=%s"; static char *ensemblGeneIdUrl = "http://www.ensembl.org/%s/Gene/Summary?db=core;t=%s"; static char *ensemblProteinIdUrl = "http://www.ensembl.org/%s/Transcript/ProteinSummary?db=core;t=%s"; static char *ensemblSupportingEvidUrl = "http://www.ensembl.org/%s/Transcript/SupportingEvidence?db=core;t=%s"; static char *ensemblH37TranscriptIdUrl = "http://grch37.ensembl.org/%s/Transcript/Summary?db=core;t=%s"; static char *ensemblH37GeneIdUrl = "http://grch37.ensembl.org/%s/Gene/Summary?db=core;t=%s"; static char *ensemblH37ProteinIdUrl = "http://grch37.ensembl.org/%s/Transcript/ProteinSummary?db=core;t=%s"; static char *ensemblH37SupportingEvidUrl = "http://grch37.ensembl.org/%s/Transcript/SupportingEvidence?db=core;t=%s"; -static char *vegaTranscriptIdUrl = "http://vega.sanger.ac.uk/%s/Transcript/Summary?db=core;t=%s"; -static char *vegaGeneIdUrl = "http://vega.sanger.ac.uk/%s/Gene/Summary?db=core;g=%s"; - static char *gencodeBiotypesUrl = "http://www.gencodegenes.org/pages/biotypes.html"; static char *gencodeTagsUrl = "http://www.gencodegenes.org/pages/tags.html"; static char *yalePseudoUrl = "http://tables.pseudogene.org/%s"; static char *hgncUrl = " https://www.genenames.org/data/gene-symbol-report/#!/symbol/%s"; static char *geneCardsUrl = "http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s"; static char *apprisHomeUrl = "http://appris-tools.org/"; static char *apprisGeneUrl = "http://appris-tools.org/#/database/id/%s/%s?sc=ensembl"; static char *getBaseAcc(char *acc, char *accBuf, int accBufSize) /* get the accession with version number dropped. */ { safecpy(accBuf, accBufSize, acc); char *dot = strchr(accBuf, '.'); if (dot != NULL) @@ -255,48 +252,48 @@ safef(urlBuf, sizeof(urlBuf), urlTemplate, id); printf("<a href=\"%s\" target=_blank>%s</a>", urlBuf, id); } } #if UNUSED static void prTdExtIdAnchor(char *id, char *urlTemplate) /* print a table data element with an anchor for a id */ { printf("<td>"); prExtIdAnchor(id, urlTemplate); } #endif static void prEnsIdAnchor(char *id, char *urlTemplate) -/* if an id to an ensembl or vega database is not empty, print an HTML anchor to it */ +/* if an id to an ensembl database is not empty, print an HTML anchor to it */ { if (!isEmpty(id)) { char idBuf[64], urlBuf[512]; /* The lift37 releases append a '_N' modifier to the ids to indicate the are * mapped. N is an integer mapping version. Don't include this in link if it exists. */ safecpy(idBuf, sizeof(idBuf), id); char *p = strchr(idBuf, '_'); if (p != NULL) *p = '\0'; safef(urlBuf, sizeof(urlBuf), urlTemplate, getScientificNameSym(), idBuf); printf("<a href=\"%s\" target=_blank>%s</a>", urlBuf, id); } } static void prTdEnsIdAnchor(char *id, char *urlTemplate) -/* print a table data element with an ensembl/vega anchor for a id */ +/* print a table data element with an ensembl anchor for a id */ { printf("<td>"); prEnsIdAnchor(id, urlTemplate); } static void prApprisTdAnchor(char *id, char *label, char *urlTemplate) /* print a gene or transcript link to APPRIS */ { // under bar separated, lower case species name. char *speciesArg = hScientificName(database); toLowerN(speciesArg, strlen(speciesArg)); subChar(speciesArg, ' ', '_'); char accBuf[64]; printf("<td><a href=\""); @@ -396,32 +393,32 @@ if (transAttrs->proteinId != NULL) { // protein id in database, maybe not for this transcript printf("<tr><th>Protein id"); if (strlen(transAttrs->proteinId) > 0) prTdEnsIdAnchor(transAttrs->proteinId, (isGrcH37Native(tdb) ? ensemblH37ProteinIdUrl: ensemblProteinIdUrl)); else printf("<td> "); printf("<td>"); printf("</tr>\n"); } printf("<tr><th>HAVANA manual id"); -prTdEnsIdAnchor(transAttrs->havanaTranscriptId, vegaTranscriptIdUrl); -prTdEnsIdAnchor(transAttrs->havanaGeneId, vegaGeneIdUrl); +printf("<td>%s", transAttrs->havanaTranscriptId); +printf("<td>%s", transAttrs->havanaGeneId); printf("</tr>\n"); printf("<tr><th>Position"); printf("<td>"); writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd); printf("<td>"); writePosLink(transAnno->chrom, geneChromStart, geneChromEnd); printf("</tr>\n"); printf("<tr><th>Strand<td>%s<td></tr>\n", transAnno->strand); printf("<tr><th><a href=\"%s\" target = _blank>Biotype</a><td>%s<td>%s</tr>\n", gencodeBiotypesUrl, transAttrs->transcriptType, transAttrs->geneType); printf("<tr><th>Annotation Level<td>%s (%d)<td></tr>\n", getLevelDesc(transAttrs->level), transAttrs->level);