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/* File: translate.c
* Author: sre, 1993-01-12
* Copyright (c) 2010 - 2012 Genome Research Ltd
* ---------------------------------------------------------------------------
* SeqTools is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 3
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
* or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
* ---------------------------------------------------------------------------
* This file is part of the SeqTools sequence analysis package,
* written by
* Gemma Barson (Sanger Institute, UK) <gb10@sanger.ac.uk>
*
* based on original code by
* Erik Sonnhammer (SBC, Sweden) <Erik.Sonnhammer@sbc.su.se>
*
* and utilizing code taken from the AceDB and ZMap packages, written by
* Richard Durbin (Sanger Institute, UK) <rd@sanger.ac.uk>
* Jean Thierry-Mieg (CRBM du CNRS, France) <mieg@kaa.crbm.cnrs-mop.fr>
* Ed Griffiths (Sanger Institute, UK) <edgrif@sanger.ac.uk>
* Roy Storey (Sanger Institute, UK) <rds@sanger.ac.uk>
* Malcolm Hinsley (Sanger Institute, UK) <mh17@sanger.ac.uk>
*
* Description: Functions for complementing, reversing and translating nucleic
* acid sequences
*
* Exported functions: See utilities.h
*----------------------------------------------------------------------------
*/
#include <seqtoolsUtils/utilities.hpp>
#include <seqtoolsUtils/iupac.hpp>
#include <glib.h>
#include <ctype.h>
#include <string.h>
/* Translation errors domain */
#define SEQTOOLS_TRANSLATION_ERROR g_quark_from_string("SeqTools")
/* Error codes */
typedef enum
{
SEQTOOLS_ERROR_INVALID_NUCLEOTIDE /* invalid dna/rna nucleotide */
} SeqToolsTranslationError;
/* THIS FILE NEEDS RENAMING TO SOMETHING LIKE utils.c */
/* Function: Translate(char *seq, char **code)
*
* Given a ptr to the start of a nucleic acid sequence, and a genetic code, translate the sequence
* into amino acid sequence.
*
* code is an array of 65 strings, representing the translations of the 64 codons, arranged in
* order AAA, AAC, AAG, AAU, ..., UUA, UUC, UUG, UUU. '*' or '***' is used to represent
* termination codons, usually. The final string, code[64], is the code for an ambiguous amino
* acid.
*
* Because of the way space is allocated for the amino acid sequence, the amino acid strings
* cannot be longer than 3 letters each. (I don't foresee using anything but the single- and
* triple- letter codes.)
*
* Returns a ptr to the translation string on success, or NULL on failure.
*/
char *blxTranslate(const char *seq, char **code)
{
char *aaseq = NULL ; /* RETURN: the translation */
int codon; /* index for codon */
char *aaptr; /* ptr into aaseq */
int i;
if (seq && *seq)
{
aaseq = (char *)g_malloc(strlen(seq) + 1) ;
for (aaptr = aaseq ; *seq != '\0' && *(seq+1) != '\0' && *(seq+2) != '\0'; seq += 3)
{
/* calculate the lookup value for this codon */
codon = 0;
for (i = 0; i < 3; i++)
{
codon *= 4;
switch (*(seq + i))
{
case 'A': case 'a': break;
case 'C': case 'c': codon += 1; break;
case 'G': case 'g': codon += 2; break;
case 'T': case 't': codon += 3; break;
case 'U': case 'u': codon += 3; break;
default: codon = 64; break;
}
if (codon == 64)
break;
}
strcpy(aaptr, code[codon]);
aaptr += strlen(code[codon]);
}
}
return aaseq ;
}
/* Get the complement of the given nucleotide. Returns the original char and sets
* the error if no valid complement exists */
char complementChar(const char inputChar, GError **error)
{
/* Loop through each iupac code looking for this char. iupac chars are all
* uppercase */
char result = '\0';
char c = toupper(inputChar);
int idx = 0;
for ( ; c != iupac[idx].sym && idx < IUPACSYMNUM; idx++);
if (idx >= IUPACSYMNUM)
{
/* not found; return original char */
result = inputChar;
g_set_error(error, SEQTOOLS_TRANSLATION_ERROR, SEQTOOLS_ERROR_INVALID_NUCLEOTIDE, "Invalid nucleotide '%c'; could not find complement.\n", inputChar);
}
else
{
result = iupac[idx].symcomp;
if (islower(inputChar))
result = tolower(result);
}
return result;
}
/* All these calls need rationalising into a single function with options. */
/* revComplement.c
*
* Reverse complement of a IUPAC character string
*
*/
/* Ratinalise this with my func. below..... */
char *revComplement(char *comp, char *seq)
{
long bases;
char *bckp, *fwdp;
long pos;
if (comp == NULL)
return NULL;
if (seq == NULL)
return NULL;
bases = strlen(seq);
fwdp = comp;
bckp = seq + bases -1;
for (pos = 0; pos < bases; pos++)
{
*fwdp = complementChar(*bckp, NULL);
fwdp++;
bckp--;
}
*fwdp = '\0';
return comp;
}
/* blxComplement.c
*
* Just complement of a IUPAC character string
*
* Note that it overwrites calling string!!!! (revcomp doesn't)
*/
void blxComplement(char *seq)
{
char *fwdp;
long pos;
if (seq == NULL)
return ;
fwdp = seq;
for (pos = 0; pos < (int)strlen(seq); pos++)
{
*fwdp = complementChar(*fwdp, NULL);
fwdp++;
}
*fwdp = '\0';
return ;
}
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