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/inc/genePred.h src/hg/inc/genePred.h
index 5a8204b..c03aba0 100644
--- src/hg/inc/genePred.h
+++ src/hg/inc/genePred.h
@@ -1,317 +1,320 @@
/* genePred.h was originally generated by the autoSql program, which also
* generated genePred.c and genePred.sql. This header links the database and the RAM
* representation of objects. */
+/* Copyright (C) 2013 The Regents of the University of California
+ * See README in this or parent directory for licensing information. */
+
#ifndef GENEPRED_H
#define GENEPRED_H
#include "dnaseq.h"
struct gff;
struct gffFile;
struct gffGroup;
struct psl;
struct genbankCds;
struct rbTree;
enum cdsStatus
/* value to indicate status of CDS annotation at either start or end */
{
cdsNone, /* "none" - No CDS (non-coding) */
cdsUnknown, /* "unk" - CDS is unknown (coding, but not known) */
cdsIncomplete, /* "incmpl" - CDS is not complete at this end */
cdsComplete, /* "cmpl" - CDS is complete at this end */
};
enum genePredCreateOpts
/* bit set of options for genePredGetCreateSql */
{
genePredBasicSql = 0x00, /* used if nothing special */
genePredWithBin = 0x01 /* create bin column */
};
enum genePredFromPslOpts
/* bit set of options for genePredFromPsl3 */
{
genePredPslDefaults = 0x00, /* used if nothing special */
genePredPslCdsMod3 = 0x01 /* only merge gaps in CDS if mod 3 */
};
enum genePredFromGxfOpts
/* bit set of options for genePredFromGroupedGff/genePredFromGroupedGtf */
{
genePredGxfDefaults = 0x00, /* used if nothing special */
genePredGxfImpliedStopAfterCds = 0x01, /* stop codon is implied outside of
* the annotated CDS bounds */
genePredGxfGeneNameAsName2 = 0x02 /* use gene_name instead of gene_id
* for name2 */
};
enum genePredFields
/* Bit set to indicate which optional fields are used.
* N.B. value order must match order in genePred */
{
genePredNoOptFld = 0x00, /* use for no opt fields */
genePredScoreFld = 0x01, /* score field */
genePredName2Fld = 0x02, /* name2 field */
genePredCdsStatFld = 0x04, /* cdsStart/EndStat fields */
genePredExonFramesFld = 0x08, /* exonFrames field */
genePredAllFlds = 0xFF /* include all extended fields */
};
struct genePred
/* A gene prediction, with optional fields. */
{
struct genePred *next; /* Next in singly linked list. */
char *name; /* Name of loci, transcript, mRNA, etc */
char *chrom; /* Chromosome name */
char strand[2]; /* + or - for strand */
unsigned txStart; /* Transcription start position */
unsigned txEnd; /* Transcription end position */
unsigned cdsStart; /* Coding region start */
unsigned cdsEnd; /* Coding region end */
unsigned exonCount; /* Number of exons */
unsigned *exonStarts; /* Exon start positions */
unsigned *exonEnds; /* Exon end positions */
/* optional fields */
unsigned optFields; /* which optional fields are used (not in
* database) */
int score; /* score */
char *name2; /* Secondary name. (e.g. name of gene), or
* empty if none, NULL if field not
* requested */
enum cdsStatus cdsStartStat; /* Status of cdsStart annotation */
enum cdsStatus cdsEndStat; /* Status of cdsEnd annotation */
int *exonFrames; /* List of frame for each exon, or -1
* if no frame or not known. NULL if not
* available. */
};
/* Standard value to use for insertMergeSize when creating genePred.
* Set to 8 due to microdeletions.
*/
#define genePredStdInsertMergeSize 8
#define GENEPRED_NUM_COLS 10 /* number of columns in a genePred */
#define GENEPREDX_NUM_COLS 15 /* max number of columns in extended genePred */
struct genePred *genePredLoad(char **row);
/* Load a genePred from row fetched with select * from genePred
* from database. Dispose of this with genePredFree().
* NOTE: cannabalizes the row argument */
struct genePred *genePredLoadAll(char *fileName);
/* Load all genePred from whitespace-separated file.
* Dispose of this with genePredFreeList(). */
struct genePred *genePredLoadAllByChar(char *fileName, char chopper);
/* Load all genePred from chopper separated file.
* Dispose of this with genePredFreeList(). */
#define genePredLoadAllByTab(a) genePredLoadAllByChar(a, '\t');
/* Load all genePred from tab separated file.
* Dispose of this with genePredFreeList(). */
struct genePred *genePredCommaIn(char **pS, struct genePred *ret);
/* Create a genePred out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new genePred */
void genePredFree(struct genePred **pEl);
/* Free a single dynamically allocated genePred such as created
* with genePredLoad(). */
void genePredFreeList(struct genePred **pList);
/* Free a list of dynamically allocated genePred's */
void genePredOutput(struct genePred *el, FILE *f, char sep, char lastSep);
/* Print out genePred. Separate fields with sep. Follow last field with lastSep. */
#define genePredTabOut(el,f) genePredOutput(el,f,'\t','\n')
/* Print out genePred as a line in a tab-separated file. */
#define genePredCommaOut(el,f) genePredOutput(el,f,',',',')
/* Print out genePred as a comma separated list including final comma. */
/* --------- Start of hand generated code. ---------------------------- */
struct genePred *genePredExtLoad(char **row, int numCols);
/* Load a genePred with from a row, with optional fields. The row must
* contain columns in the order in the struct, and they must be present up to
* the last specfied optional field. Missing intermediate fields must have
* zero or empty columns, they may not be omitted. Fields at the end can be
* omitted. Dispose of this with genePredFree(). */
struct genePred *genePredExtLoadAll(char *fileName);
/* Load all genePreds with from tab-separated file, possibly with optional
* fields. Dispose of this with genePredFreeList(). */
char *genePredCdsStatStr(enum cdsStatus stat);
/* get string value of a cdsStatus */
void genePredAddGenbankCds(struct psl *psl, struct genbankCds* cds,
struct genePred *gene);
/* Convert cdsStart/End from mrna to genomic coordinates.
* Note that the genePred blocks need not be filled in before
* this call. */
int genePredCmp(const void *va, const void *vb);
/* Compare to sort based on chromosome, txStart. */
int genePredNameCmp(const void *va, const void *vb);
/* Compare to sort based on name, then chromosome, txStart. */
struct genePred *genePredFromGroupedGff(struct gffFile *gff, struct gffGroup *group,
char *name, char *exonSelectWord, unsigned optFields,
unsigned options);
/* Convert gff->groupList to genePred list. Only put lines where feature type matches
* exonSelectWord into the gene. (If exonSelectWord is NULL, all go in)
* If optFields contains the bit set of optional fields to add to the genePred.
* If genePredCdsStatFld is set, then the CDS status information is
* set based on the presences of start_codon, stop_codon, and CDS features.
* If genePredExonFramesFld is set, then frame is set as specified in the GTF.
* Options are from genePredFromGxfOpts. If genePredGxfImpliedStopAfterCds
* is specified, it is treated as if a stop_codon annotation was found,
* if there isn't one. If genePredGxfGeneNameAsName2 is specified, use
* gene_name for the name2 field otherwise gene_id.
*/
struct genePred *genePredFromGroupedGtf(struct gffFile *gff, struct gffGroup *group, char *name,
unsigned optFields, unsigned options);
/* Convert gff->groupList to genePred list, using GTF feature conventions;
* including the stop codon in the 3' UTR, not the CDS (grr). Assumes
* gffGroup is sorted in assending coords, with overlaping starts sorted by
* end coords, which is true if it was created by gffGroupLines(). If
* optFields contains the bit set of optional fields to add to the genePred.
* If genePredName2Fld is specified, then the gene_id is used for the name2
* field. If genePredCdsStatFld is set, then the CDS status information is
* set based on the presences of start_codon, stop_codon, and CDS features.
* If genePredExonFramesFld is set, then frame is set as specified in the GTF.
* Options are from genePredFromGxfOpts. If genePredGxfImpliedStopAfterCds
* is specified, it is treated as if a stop_codon annotation was found,
* if there isn't one.
*/
struct genePred *genePredFromPsl3(struct psl *psl, struct genbankCds* cds,
unsigned optFields, unsigned options,
int cdsMergeSize, int utrMergeSize);
/* Convert a PSL of an mRNA alignment to a genePred, converting a genbank CDS
* specification string to genomic coordinates. Small genomic inserts are
* merged based on the mergeSize parameters. Gaps no larger than the
* specified merge sizes result in the adjacent blocks being merged into a
* single exon. Gaps in CDS use cdsMergeSize, in UTR use utrMergeSize. If
* the genePredPslCdsMod3 option is specified, then CDS gaps are only merged
* if a multiple of three. A negative merge sizes disables merging of blocks.
* This differs from specifying zero in that adjacent blocks will not be
* merged. The optfields field is a set from genePredFields, indicated what
* fields to create. Zero-length CDS, or null cds, creates without CDS
* annotation. If cds is null, it will set status fields to cdsNone. */
struct genePred *genePredFromPsl2(struct psl *psl, unsigned optFields,
struct genbankCds* cds, int insertMergeSize);
/* Compatibility function, genePredFromPsl3 is prefered. See that function's
* documentation for details. This calls genePredFromPsl3 with no options
* and insertMergeSize set for CDS and UTR.
*/
struct genePred *genePredFromPsl(struct psl *psl, int cdsStart, int cdsEnd,
int insertMergeSize);
/* Compatibility function, genePredFromPsl3 is prefered. See that function's
* documentation for details. This calls genePredFromPsl3 with no options.
*/
char* genePredGetCreateSql(char* table, unsigned optFields, unsigned options,
int chromIndexLen);
/* Get SQL required to create a genePred table. optFields is a bit set
* consisting of the genePredFields values. Options are a bit set of
* genePredCreateOpts. Returned string should be freed. This will create all
* optional fields that preceed the highest optFields column. chromIndexLen
* is now ignored.. */
struct genePred *getOverlappingGene(char *db, struct genePred **list, char *table, char *chrom, int cStart, int cEnd, char *name, int *retOverlap);
/* read all genes from a table find the gene with the biggest overlap.
* Cache the list of genes to so we only read it once.
* If there are multiple hits and the name that matches exactly,
* this overrides the biggest overlap */
int genePredBases(struct genePred *gp);
/* count coding and utr bases in a gene prediction */
int genePredCodingBases(struct genePred *gp);
/* Count up the number of coding bases in gene prediction. */
boolean genePredCdsExon(struct genePred *gp, int iExon, int *startPtr, int *endPtr);
/* Get the CDS range in an exon. If there is no CDS, return FALSE and then
* set start == end */
int genePredCheck(char *desc, FILE* out, int chromSize,
struct genePred* gp);
/* Validate a genePred for consistency. desc is printed the error messages
* to file out (open /dev/null to discard). chromSize should contain
* size of chromosome, or 0 if chrom is not valid, or -1 to not check
* chromosome bounds. Returns count of errors. */
boolean genePredNmdTarget(struct genePred *gp);
/* Return TRUE if cds end is more than 50bp upstream of
last intron. */
void genePredAddExonFrames(struct genePred *gp);
/* Add exonFrames array to a genePred that doesn't have it. Frame is assumed
* to be contiguous. */
void genePredRc(struct genePred *gp, int chromSize);
/* Reverse complement a genePred (project it to the opposite strand). Useful
* when doing analysis that is simplified by having things on the same strand.
*/
int genePredCdsSize(struct genePred *gp);
/* compute the number of bases of CDS */
struct genePred *genePredNew(char *name, char *chrom, char strand,
unsigned txStart, unsigned txEnd,
unsigned cdsStart, unsigned cdsEnd,
unsigned optFields, unsigned exonSpace);
/* create a new gene with space for the specified number of exons allocated.
* genePredGrow maybe used to expand this space if needed. */
void genePredGrow(struct genePred *gp, unsigned *exonSpacePtr);
/* Increase memory allocated to a psl to hold more exons. exonSpacePtr
* should point the the current maximum number of exons and will be
* updated to with the new amount of space. */
struct rbTree *genePredToRangeTree(struct genePred *gp, boolean cdsOnly);
/* Convert genePred into a range tree. */
void gpPartOutAsBed(struct genePred *gp, int start, int end, FILE *f,
char *type, int id, int minSize);
/* Write out part of gp as bed12. */
boolean codonToPos(struct genePred *gp, unsigned num, int *chromStart, int *chromEnd);
// map 1-based codon to genomic coordinates. If the codon crosses an exon junction, we return just the beginning (LHS) of the codon.
// Returns true if we find the codon in given gene predition; chromStart and chromEnd are set to appropriate three base region.
boolean exonToPos(struct genePred *gp, unsigned num, int *chromStart, int *chromEnd);
// map 1-based exon number to genomic coordinates.
// Returns true if we find the exon in given gene predition; chromStart and chromEnd are set to appropriate region.
struct asObject *genePredAsObj();
// Return asObject describing fields of genePred
struct dnaSeq *genePredGetDna(char *database, struct genePred *gp,
boolean coding, enum dnaCase dnaCase);
// Returns the DNA sequence associated with gene prediction.
// Negative strand genes will return the sequence as read from the negative strand.
// Optionally restrict to coding sequence only
int genePredBaseToCodingPos(struct genePred *gp, int basePos,
boolean stranded, boolean *isCoding);
// Given a genePred model and a single (0 based) base position, predict the 0-based
// DNA (stranded) coding sequence pos. Dividing this number by 3 should give the AA position!
// Returns -1 when outside of coding exons unless OPTIONAL isCoding pointer to boolean is
// provided. In that case, returns last valid position and sets isCoding to FALSE.
#endif /* GENEPRED_H */