[Bio] / FigKernelScripts / gjoseqlib.h Repository:
ViewVC logotype

View of /FigKernelScripts/gjoseqlib.h

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Mon Jun 11 20:08:03 2012 UTC (7 years, 5 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2014_0729, rast_rel_2014_0912, HEAD
Support for codon usage analyses.

/*
 *   gjoseqlib.h
 */

#ifndef GJOSEQLIB_H
#define GJOSEQLIB_H

typedef struct sequence
{
    size_t  id_len;
    char   *id;
    size_t  def_len;
    char   *def;
    size_t  seq_len;
    char   *seq;
} seq_t, *seqptr_t;

typedef  char*  gencode_t;


#define DUMPSEQ(seq)  fprintf( stderr, "%d: %s\n%d:%s\n%d: %s\n", seq->id_len, seq->id, seq->def_len, seq->def, seq->seq_len, seq->seq );

seq_t *
new_sequence_by_sizes( size_t id_len, size_t def_len, size_t seq_len );

seq_t *
copy_sequence( seq_t *entry );

void
free_sequence( seq_t *entry );

void
seq_toupper( seq_t *entry );

void
seq_tolower( seq_t *entry );

char *
complement_DNA_seq( char *seq );

char *
complement_RNA_seq( char *seq );

seq_t *
complement_DNA( seq_t *entry );

seq_t *
complement_RNA( seq_t *entry );

void
init_local_gencode( int codenum );

gencode_t
get_gencode( int NCBI_code );

char
translate_3_nt( int n1, int n2, int n3, gencode_t gencode );

char
translate_codon( char *codon, gencode_t gencode );

char *
translate_seq_with_code( char *nt_seq, int met, int NCBI_code );

char *
translate_seq( char *nt_seq, int met );

seq_t *
translate_entry_with_code( seq_t *entry, int met, int NCBI_code );

seq_t *
translate_entry( seq_t *entry, int met );

#endif

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3