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esl_gencode.h
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esl_gencode.h
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/* Genetic code tables for translation, whether canonical or non.
*/
#ifndef eslGENCODE_INCLUDED
#define eslGENCODE_INCLUDED
#include "esl_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_fileparser.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_getopts.h"
typedef struct {
int transl_table; // NCBI transl_table number, or -1. Only set for a standard NCBI table, with _Set(); _Read() from file doesn't set this.
char desc[128]; // Description, or "". ... ditto
ESL_DSQ basic[64]; // Basic code table. aacode[0..63; pos1^16 + pos2^4 + pos3] = residue code for amino acid, 0..19 or the Nonresidue code. No degeneracies.
int8_t is_initiator[64]; // TRUE for allowed initiator codons; FALSE if not
const ESL_ALPHABET *nt_abc; // A reference to nucleic alphabet that caller is maintaining elsewhere
const ESL_ALPHABET *aa_abc; // A reference to amino alphabet that caller is maintaining
} ESL_GENCODE;
/* struct esl_gencode_workstate_s
* keeps state in DNA sequence <sq>, allowing us to process a sequence
* either in a single gulp (using ReadSeq) or in overlapping windows
* (using ReadWindow).
*
* also contains one-time configuration information for translation
*/
typedef struct esl_gencode_workstate_s {
/* stateful info (which may get updated with each new seq, strand, and/or window): */
ESL_SQ *psq[3]; // Growing ORFs in each frame
int8_t in_orf[3]; // TRUE|FALSE: TRUE if we're growing an ORF in this frame
int apos; // 1..L: current nucleotide we're on (starting a codon) in <sq>
int frame; // 0..2: which frame <apos> is in
int codon; // 0..63: Digitized codon for apos,apos+1,apos+2
int inval; // 0..3: how many apos increments we need to get past an ambiguous nucleotide
int is_revcomp; // TRUE|FALSE: TRUE if we're doing reverse complement strand
int orfcount; // >=0: How many ORFs we've processed so far
ESL_SQ_BLOCK *orf_block; // block of sequences to which to write ORFs
/* one-time configuration information (from options) */
int do_watson; // TRUE|FALSE: TRUE if we translate the top strand
int do_crick; // TRUE|FALSE: TRUE if we translate the reverse complement strand
int using_initiators; // TRUE|FALSE : TRUE if -m or -M, only valid initiators can start an ORF, and initiator codon always translates to Met
int minlen; // >=0: minimum orf length that process_orf will deal with
FILE *outfp; // default stdout: where to write output ORF data
int outformat; // default eslSQFILE_FASTA: sqfile format to write ORFs in
} ESL_GENCODE_WORKSTATE;
/* Create/Destroy workstate */
extern void esl_gencode_WorkstateDestroy(ESL_GENCODE_WORKSTATE *wrk);
extern ESL_GENCODE_WORKSTATE * esl_gencode_WorkstateCreate(ESL_GETOPTS *go, ESL_GENCODE *gcode);
/* the ESL_GENCODE genetic code object */
extern ESL_GENCODE *esl_gencode_Create(const ESL_ALPHABET *nt_abc, const ESL_ALPHABET *aa_abc);
extern void esl_gencode_Destroy (ESL_GENCODE *gcode);
extern int esl_gencode_Set (ESL_GENCODE *gcode, int ncbi_transl_table);
extern int esl_gencode_SetInitiatorAny (ESL_GENCODE *gcode);
extern int esl_gencode_SetInitiatorOnlyAUG(ESL_GENCODE *gcode);
/* reading and writing genetic codes in NCBI format */
extern int esl_gencode_Read(ESL_FILEPARSER *efp, const ESL_ALPHABET *nucleic_abc, const ESL_ALPHABET *amino_abc, ESL_GENCODE **ret_gcode);
extern int esl_gencode_Write(FILE *ofp, const ESL_GENCODE *gcode, int add_comment);
/* DNA->protein digital translation, allowing ambiguity chars */
extern int esl_gencode_GetTranslation(const ESL_GENCODE *gcode, ESL_DSQ *dsqp);
extern int esl_gencode_IsInitiator (const ESL_GENCODE *gcode, ESL_DSQ *dsqp);
/* Debugging/development utilities */
extern char *esl_gencode_DecodeDigicodon(const ESL_GENCODE *gcode, int digicodon, char *codon);
extern int esl_gencode_DumpAltCodeTable(FILE *ofp);
extern int esl_gencode_Compare(const ESL_GENCODE *gc1, const ESL_GENCODE *gc2, int metadata_too);
/* Functions for processing ORFs */
extern int esl_gencode_ProcessOrf(ESL_GENCODE_WORKSTATE *wrk, ESL_SQ *sq);
extern void esl_gencode_ProcessStart(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQ *sq);
extern int esl_gencode_ProcessPiece(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQ *sq);
extern int esl_gencode_ProcessEnd(ESL_GENCODE_WORKSTATE *wrk, ESL_SQ *sq);
#endif /*eslGENCODE_INCLUDED*/