/* retroMrnaInfo.h was originally generated by the autoSql program, which also * generated retroMrnaInfo.c and retroMrnaInfo.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef RETROMRNAINFO_H #define RETROMRNAINFO_H #ifndef JKSQL_H #include "jksql.h" #endif #define RETROMRNAINFO_NUM_COLS 57 struct retroMrnaInfo /* Retrogenes based on cDNA alignments that are expressed or processed pseudogenes. */ { struct retroMrnaInfo *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold col1 */ unsigned chromStart; /* pseudogene alignment start position col2 */ unsigned chromEnd; /* pseudogene alignment end position col3 */ char *name; /* Name of pseudogene col4 */ unsigned score; /* score of pseudogene with gene col5 */ char strand[3]; /* + or - */ unsigned thickStart; /* Start of where display should be thick (start codon) */ unsigned thickEnd; /* End of where display should be thick (stop codon) */ unsigned reserved; /* Always zero for now */ int blockCount; /* Number of blocks */ int *blockSizes; /* Comma separated list of block sizes */ int *chromStarts; /* Start positions relative to chromStart */ int retroExonCount; /* number of exons in retroGene col13 */ int axtScore; /* blastz score, parent mrna aligned to pseudogene col14 */ char *type; /* type of evidence col15 */ char *gChrom; /* Chromosome name col16 */ int gStart; /* gene alignment start position col17 */ int gEnd; /* gene alignment end position col18 */ char gStrand[3]; /* strand of gene col19 */ unsigned parentSpliceCount; /* # of splice sites in parent gene col20 */ unsigned geneOverlap; /* bases overlapping col21 */ unsigned polyA; /* count of As in polyA col22 */ int polyAstart; /* start of polyA, relative to end of pseudogene col23 */ int exonCover; /* number of exons in Gene covered col24 */ unsigned intronCount; /* number of introns in pseudogene col25 */ unsigned bestAliCount; /* number of good mrnas aligning col26 */ unsigned matches; /* matches + repMatches col27 */ unsigned qSize; /* aligning bases in pseudogene col28 */ unsigned qEnd; /* end of cdna alignment col29 */ unsigned tReps; /* repeats in gene col30 */ int overlapRhesus; /* percent of retro that breaks net relative to Rhesus col31 */ int overlapMouse; /* percent of retro that breaks net relative to Mouse col32 */ unsigned coverage; /* % of bases that align to gene col33 */ int label; /* 1=pseudogene,-1 not pseudogene -2 expressed retroGene col34 */ unsigned milliBad; /* milliBad score, pseudogene aligned to genome col35 */ unsigned oldScore; /* another heuristic col36 */ int oldIntronCount; /* old simple intron count col37 */ int processedIntrons; /* count of introns removed via retrotransposition col38 */ int conservedSpliceSites; /* conserved splice site count col39 */ int maxOverlap; /* largest overlap with another mrna col40 */ char *refSeq; /* Name of closest regSeq to gene col41 */ int rStart; /* refSeq alignment start position col42 */ int rEnd; /* refSeq alignment end position col43 */ char *mgc; /* Name of closest mgc to gene col44 */ int mStart; /* mgc alignment start position col45 */ int mEnd; /* mgc alignment end position col46 */ char *kgName; /* Name of closest knownGene to gene col47 */ int kStart; /* kg alignment start position col48 */ int kEnd; /* kg alignment end position col49 */ char *overName; /* name of overlapping mrna col50 */ int overStart; /* overlapping mrna start position col51 */ int overExonCover; /* count of overlapping mrna exons col52 */ char overStrand[3]; /* strand of overlapping mrna col53 */ int overlapDog; /* percent of retro that breaks net relative to dog col54 */ float posConf; /* pvalue for positive col55 */ unsigned polyAlen; /* length of polyA col56 */ float kaku; /* ratio of substitutions between coding and utr wrt parent gene */ }; struct retroMrnaInfo *retroMrnaInfoLoad(char **row); struct retroMrnaInfo *retroMrnaInfo56Load(char **row); /* Load a retroMrnaInfo from row fetched with select * from retroMrnaInfo * from database. Dispose of this with retroMrnaInfoFree(). */ struct retroMrnaInfo *retroMrnaInfoLoadAll(char *fileName); /* Load all retroMrnaInfo from whitespace-separated file. * Dispose of this with retroMrnaInfoFreeList(). */ struct retroMrnaInfo *retroMrnaInfoLoadAllByChar(char *fileName, char chopper); /* Load all retroMrnaInfo from chopper separated file. * Dispose of this with retroMrnaInfoFreeList(). */ #define retroMrnaInfoLoadAllByTab(a) retroMrnaInfoLoadAllByChar(a, '\t'); /* Load all retroMrnaInfo from tab separated file. * Dispose of this with retroMrnaInfoFreeList(). */ struct retroMrnaInfo *retroMrnaInfoLoadByQuery(struct sqlConnection *conn, char *query); /* Load all retroMrnaInfo from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with retroMrnaInfoFreeList(). */ void retroMrnaInfoSaveToDb(struct sqlConnection *conn, struct retroMrnaInfo *el, char *tableName, int updateSize); /* Save retroMrnaInfo as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ struct retroMrnaInfo *retroMrnaInfoCommaIn(char **pS, struct retroMrnaInfo *ret); /* Create a retroMrnaInfo out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new retroMrnaInfo */ void retroMrnaInfoFree(struct retroMrnaInfo **pEl); /* Free a single dynamically allocated retroMrnaInfo such as created * with retroMrnaInfoLoad(). */ void retroMrnaInfoFreeList(struct retroMrnaInfo **pList); /* Free a list of dynamically allocated retroMrnaInfo's */ void retroMrnaInfoOutput(struct retroMrnaInfo *el, FILE *f, char sep, char lastSep); /* Print out retroMrnaInfo. Separate fields with sep. Follow last field with lastSep. */ #define retroMrnaInfoTabOut(el,f) retroMrnaInfoOutput(el,f,'\t','\n'); /* Print out retroMrnaInfo as a line in a tab-separated file. */ #define retroMrnaInfoCommaOut(el,f) retroMrnaInfoOutput(el,f,',',','); /* Print out retroMrnaInfo as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ struct retroMrnaInfo *retroMrnaInfoQuery(struct sqlConnection *conn, char *table, char *mappedId); /* load a single transMapInfo object for an mapped id from a table, * or error if not found */ #endif /* RETROMRNAINFO_H */