a93daa92b77f5717f8ff247cb049a46cd0f66409 markd Sun Aug 21 17:37:28 2022 -0700 add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column diff --git src/hg/inc/encode/wgEncodeGencodeAttrs.h src/hg/inc/encode/wgEncodeGencodeAttrs.h index 6c5f4bb..063d51c 100644 --- src/hg/inc/encode/wgEncodeGencodeAttrs.h +++ src/hg/inc/encode/wgEncodeGencodeAttrs.h @@ -1,77 +1,73 @@ /* wgEncodeGencodeAttrs.h was originally generated by the autoSql program, which also * generated wgEncodeGencodeAttrs.c and wgEncodeGencodeAttrs.sql. This header links the database and * the RAM representation of objects. */ #ifndef WGENCODEGENCODEATTRS_H #define WGENCODEGENCODEATTRS_H -#define WGENCODEGENCODEATTRS_NUM_COLS 14 -#define WGENCODEGENCODEATTRS_NO_PROTEIN_ID_NUM_COLS 13 // older tables +#define WGENCODEGENCODEATTRS_NUM_COLS 15 +#define WGENCODEGENCODEATTRS_MIM_NUM_COLS 13 // older tables extern char *wgEncodeGencodeAttrsCommaSepFieldNames; struct wgEncodeGencodeAttrs /* Basic set of attributes associated with all Gencode transcripts. */ { struct wgEncodeGencodeAttrs *next; /* Next in singly linked list. */ char *geneId; /* Gene identifier */ char *geneName; /* Gene name */ char *geneType; /* BioType of gene */ char *geneStatus; /* Status of gene (obsolete) */ char *transcriptId; /* Transcript identifier */ char *transcriptName; /* Transcript name */ char *transcriptType; /* BioType of transcript */ char *transcriptStatus; /* Status of transcript (obsolete) */ char *havanaGeneId; /* HAVANA identifier if gene is in HAVANA */ char *havanaTranscriptId; /* HAVANA identifier if transcript is in HAVANA */ char *ccdsId; /* CCDS identifier if transcript is in CCDS */ int level; /* GENCODE level: 1 = experimental confirmed, 2 = manual, 3 = automated */ char *transcriptClass; /* high level type of transcript */ char *proteinId; /* Protein identifier (not loaded on many older versions of GENCODE) */ + int transcriptRank; /* Rank of transcript within the gene, smaller is more preferred, (not loaded on many older versions of GENCODE, in which case -1) */ }; void wgEncodeGencodeAttrsStaticLoad(char **row, int numColumns, struct wgEncodeGencodeAttrs *ret); /* Load a row from wgEncodeGencodeAttrs table into ret. The contents of ret will * be replaced at the next call to this function. */ struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsLoad(char **row, int numColumns); /* Load a wgEncodeGencodeAttrs from row fetched with select * from wgEncodeGencodeAttrs * from database. Dispose of this with wgEncodeGencodeAttrsFree(). */ struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsLoadAll(char *fileName); /* Load all wgEncodeGencodeAttrs from whitespace-separated file. * Dispose of this with wgEncodeGencodeAttrsFreeList(). */ struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsLoadAllByChar(char *fileName, char chopper); /* Load all wgEncodeGencodeAttrs from chopper separated file. * Dispose of this with wgEncodeGencodeAttrsFreeList(). */ #define wgEncodeGencodeAttrsLoadAllByTab(a) wgEncodeGencodeAttrsLoadAllByChar(a, '\t'); /* Load all wgEncodeGencodeAttrs from tab separated file. * Dispose of this with wgEncodeGencodeAttrsFreeList(). */ -struct wgEncodeGencodeAttrs *wgEncodeGencodeAttrsCommaIn(char **pS, struct wgEncodeGencodeAttrs *ret); -/* Create a wgEncodeGencodeAttrs out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new wgEncodeGencodeAttrs */ - void wgEncodeGencodeAttrsFree(struct wgEncodeGencodeAttrs **pEl); /* Free a single dynamically allocated wgEncodeGencodeAttrs such as created * with wgEncodeGencodeAttrsLoad(). */ void wgEncodeGencodeAttrsFreeList(struct wgEncodeGencodeAttrs **pList); /* Free a list of dynamically allocated wgEncodeGencodeAttrs's */ void wgEncodeGencodeAttrsOutput(struct wgEncodeGencodeAttrs *el, FILE *f, char sep, char lastSep); /* Print out wgEncodeGencodeAttrs. Separate fields with sep. Follow last field with lastSep. */ #define wgEncodeGencodeAttrsTabOut(el,f) wgEncodeGencodeAttrsOutput(el,f,'\t','\n'); /* Print out wgEncodeGencodeAttrs as a line in a tab-separated file. */ #define wgEncodeGencodeAttrsCommaOut(el,f) wgEncodeGencodeAttrsOutput(el,f,',',','); /* Print out wgEncodeGencodeAttrs as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* WGENCODEGENCODEATTRS_H */