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readseq.c
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/* File: readseq.c
* Author: Richard Durbin ([email protected])
*-------------------------------------------------------------------
* Description: generic code to read Pearson format files (fasta)
>header line
conv[x] is the internal code for char 'x'
conv[x] == -1 or -2 means ignore.
conv[x] < -2 means error.
will work on fil == stdin
* Exported functions: readSequence, writeSequence, seqConvert, readFastq, writeFastq
* HISTORY:
* Last code change: Sep 17 08:57:03 2009 (pd3)
* * Jul 29 22:42 2008 (rd): added writeFastq
* * Oct 22 06:45 2006 (rd): added readFastq
* * Dec 29 23:35 1993 (rd): now works off FILE*, returns id and desc
* Created: Tue Jan 19 21:14:35 1993 (rd)
* CVS info: $Id: readseq.c,v 1.2 2009/11/26 10:50:19 petr Exp $
*-------------------------------------------------------------------
* Copyright (c) 1993, 2006, 2008, 2009 Genome Research Limited.
*
* License:
* This file is part of fastqcheck.
*
* fastqcheck 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, see
* L<http://www.gnu.org/licenses/>.
*-------------------------------------------------------------------
*/
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#pragma inline(add)
static char *messalloc (int n)
{
char *result ;
if (!(result = (char*) malloc (n)))
{ fprintf (stderr, "MALLOC failure reqesting %d bytes - aborting\n", n) ;
exit (-1) ;
}
return result ;
}
#define messfree(x) free(x)
static void add (char c, char* *buf, int *buflen, int n)
{
if (n >= *buflen)
{
int blen = *buflen;
if (blen < 0)
{ blen = -blen ;
*buf = (char*) messalloc (blen) ;
}
else
{ blen *= 2 ;
if ((*buf = realloc(*buf,blen)) == NULL)
{ fprintf (stderr, "REALLOC failure reqesting %d bytes - aborting\n", blen) ;
exit (-1) ;
}
}
*buflen = blen;
}
(*buf)[n] = c;
}
int readSequence (FILE *fil, int *conv,
char **seq, char **id, char **desc, int *length)
{
char c ;
int n ;
static FILE *oldFil = 0 ;
static int line ;
int buflen ;
if (fil != oldFil)
{ line = 1 ;
oldFil = fil ;
}
/* get id, descriptor */
c = getc (fil) ;
if (c == '>') /* header line */
{ c = getc(fil) ;
n = 0 ; /* id */
buflen = -32;
while (!feof (fil) && c != ' ' && c != '\n' && c != '\t')
{ if (id) add (c, id, &buflen, n++) ;
c = getc (fil) ;
}
if (id) add (0, id, &buflen, n) ;
/* white space */
while (!feof (fil) && (c == ' ' || c == '\t'))
c = getc (fil) ;
n = 0 ; /* desc */
buflen = -32 ;
while (!feof (fil) && c != '\n')
{ if (desc) add (c, desc, &buflen, n++) ;
c = getc (fil) ;
}
if (desc) add (0, desc, &buflen, n) ;
++line ;
}
else
{ ungetc (c, fil) ; /* no header line */
if (id)
*id = "" ;
if (desc)
*desc = "" ;
}
/* ensure whitespace ignored */
conv[' '] = conv['\t'] = -1 ;
conv['\n'] = -3 ;
n = 0 ; /* sequence */
buflen = -1024 ;
while (!feof (fil))
{
c = getc (fil) ;
if (c == '>')
{ ungetc (c, fil) ;
break ;
}
if (c == EOF || c == EOF + 256) /* satisfies all compilers */
break ;
switch (conv[c]) {
case -2:
{ if (id)
fprintf (stderr, "Bad char 0x%x = '%c' at line %d, base %d, sequence %s\n",
c, c, line, n, *id) ;
else
fprintf (stderr, "Bad char 0x%x = '%c' at line %d, base %d\n",
c, c, line, n) ;
return 0 ;
}
break;
case -3:
++line;
case -1:
break;
default:
if (seq) add (conv[c], seq, &buflen, n++) ;
else ++n ;
}
}
if (seq) add (0, seq, &buflen, n) ;
if (length)
*length = n ;
return n ;
}
/*****************************************************/
/* a fastq block looks like:
@slxa_0020_2_0001_85
CCTTCTGCCNGCCCCCAGGAAACATTCTCATAAT
+slxa_0020_2_0001_85
???????6%"??2&?7/??'1875%?7:%)1$%2
*/
int readFastq (FILE *fil, int *conv,
char **seq, char **qval, char **id, int *length)
{
char c, *cp ;
int n, m ;
static FILE *oldFil = 0 ;
static int line ;
int buflen ;
if (fil != oldFil)
{ line = 1 ;
oldFil = fil ;
}
/* get id */
c = getc (fil) ;
if (!feof(fil) && c != '@') /* header line */
{ fprintf (stderr, "bad @ header line %d, got [0x%x] [%c]\n", line,(int)c,c) ; return -1; }
c = getc(fil) ;
n = 0 ; /* id */
buflen = -32;
while (!feof (fil) && c != '\n' ) /* the fastq identifier can contain spaces! */
{ if (id) add (c, id, &buflen, n++) ;
c = getc (fil) ;
}
if (id) add (0, id, &buflen, n) ;
if (!feof (fil) && c != '\n')
{ fprintf (stderr, "bad @ identifier line %d, got [0x%x]\n", line,(int)c) ; return -1; }
++line ;
/* ensure whitespace ignored */
conv[' '] = conv['\t'] = -1 ;
conv['\n'] = -3 ;
n = 0 ; /* sequence */
buflen = -1024 ;
while (!feof (fil))
{
c = getc (fil) ;
if (c == '+')
{ ungetc (c, fil) ;
break ;
}
if (c == EOF || c == EOF + 256) /* satisfies all compilers */
break ;
switch (conv[c]) {
case -2:
{ if (id)
fprintf (stderr, "Bad char 0x%x = '%c' at line %d, base %d, sequence %s\n",
c, c, line, n, *id) ;
else
fprintf (stderr, "Bad char 0x%x = '%c' at line %d, base %d\n",
c, c, line, n) ;
return -1;
}
break;
case -3:
++line;
case -1:
break;
default:
if (seq) add (conv[c], seq, &buflen, n++) ;
else ++n ;
}
}
if (seq) add (0, seq, &buflen, n) ;
if (length)
*length = n ;
/* second block with same identifier and matching quality values */
c = getc (fil) ;
if (!feof(fil) && c != '+') /* header line */
{ fprintf (stderr, "bad + header line %d\n", line) ; return -1; }
c = getc(fil) ; if (id) cp = *id ;
while (!feof (fil) && c != ' ' && c != '\n' && c != '\t')
{ if (id && c != *cp++)
{ fprintf (stderr, "mismatching + identifier line %d\n", line) ; return -1; }
c = getc (fil) ;
}
if (!feof (fil) && c != '\n')
{ fprintf (stderr, "bad + identifier line %d\n", line) ; return -1; }
++line ;
m = 0 ; /* qualities */
buflen = -(n+1) ;
while (!feof (fil))
{
c = getc (fil) ;
if (c == '@' && m == n)
{ ungetc (c, fil) ;
break ;
}
else if (m > n)
break ;
if (c == EOF || c == EOF + 256) /* satisfies all compilers */
break ;
if (c == '\n')
++line;
else if (qval)
add (c-33, qval, &buflen, m++) ;
else
++m ;
}
if (qval) add (0, qval, &buflen, m) ;
if (m != n)
{ fprintf (stderr, "mismatching seq, q length line %d\n", line) ; return -1; }
return n ;
}
/*****************************************************/
int seqConvert (char *seq, int *length, int *conv)
{
int i, n = 0 ;
int c ;
for (i = 0 ; seq[i] ; ++i)
{ c = seq[i] ;
if (length && i >= *length)
break ;
if (conv[c] < -2)
{ fprintf (stderr, "Bad char 0x%x = '%c' at base %d in seqConvert\n", c, c, n) ;
return 0 ;
}
if (conv[c] >= 0)
seq[n++] = conv[c] ;
}
if (n < i)
seq[n] = 0 ;
if (length)
*length = n ;
return n ;
}
/*****************************************************/
int writeSequence (FILE *fil, int *conv,
char *seq, char *id, char *desc, int len)
{
int i ;
if (!fil)
{ fprintf (stderr, "ERROR: writeSequence requires a file\n") ;
return 0 ;
}
if (id && *id)
{ fprintf (fil, ">%s", id) ;
if (desc)
fprintf (fil, " %s", desc) ;
fprintf (fil, "\n") ;
}
for (i = 0 ; i < len ; ++i)
{ if (i && !(i%60))
fputc ('\n', fil) ;
if (conv[seq[i]] > 0)
fputc (conv[seq[i]], fil) ;
else
{ fprintf (stderr, "ERROR in writeSequence: %s[%d] = %d does not convert\n",
id, i, seq[i]) ;
return 0 ;
}
}
fputc ('\n', fil) ;
return len ;
}
/*****************************************************/
int writeFastq (FILE *fil, int *conv,
char *seq, unsigned char *qual, char *id, int len)
{
int i ;
if (!fil) { fprintf (stderr, "ERROR: writeFastq requires a file\n") ; return 0 ; }
if (!id || !*id) { fprintf (stderr, "ERROR: writeFastq requires an id\n") ; return 0 ; }
fprintf (fil, "@%s\n", id) ;
for (i = 0 ; i < len ; ++i)
{ if (i && !(i%60))
fputc ('\n', fil) ;
if (conv[seq[i]] > 0)
fputc (conv[seq[i]], fil) ;
else
{ fprintf (stderr, "ERROR in writeSequence: %s[%d] = %d does not convert\n",
id, i, seq[i]) ;
return 0 ;
}
}
fputc ('\n', fil) ;
fprintf (fil, "+%s\n", id) ;
for (i = 0 ; i < len ; ++i)
{ if (i && !(i%60))
fputc ('\n', fil) ;
fputc (qual[i]+33, fil) ;
}
fputc ('\n', fil) ;
return len ;
}
/*********** read a matrix, using conv ************/
int readMatrix (char *name, int *conv, int** *mat)
{
char matdirname[256] ;
char fullname[512] ;
FILE *fil ;
char line[1024] = "#", *p;
int i, j, nsymb, smax = 0 ;
int symb[128] ;
extern char* strtok (char*, const char*) ;
if (getenv ("BLASTMAT"))
strcpy (matdirname, getenv ("BLASTMAT")) ;
else
strcpy (matdirname, "/nfs/disk100/pubseq/blastdb/") ;
strcpy (fullname, matdirname) ;
strcat (fullname, name) ;
if (!(fil = fopen (name, "r")) && !(fil = fopen (fullname, "r")))
{ fprintf (stderr, "ERROR in readMatrix: could not open %s or %s\n",
name, matdirname) ;
return 0 ;
}
while (!feof(fil) && *line == '#') /* comments */
fgets (line, 1023, fil) ;
/* character set */
p = line ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
for (i = 0 ; *p && i < 128 ; ++i)
{ symb[i] = conv[*p] ;
if (symb[i] < -2)
{ fprintf (stderr, "ERROR in readMatrix: illegal symbol %c\n", *p) ;
fclose (fil) ;
return 0 ;
}
if (symb[i] > smax)
smax = symb[i] ;
++p ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
}
nsymb = i ;
++smax ;
*mat = (int**) messalloc (smax * sizeof (int*)) ;
for (i = 0 ; i < smax ; ++i)
(*mat)[i] = (int*) messalloc (smax * sizeof (int)) ;
for (i = 0 ; fgets(line, 1023, fil) && i < nsymb ; ++i)
{ p = line ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
if (p && conv[*p] == symb[i])
{ ++p ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ; }
for (j = 0 ; *p && j < 128 ; ++j)
{ if (symb[i] >= 0 && symb[j] >= 0)
(*mat)[symb[i]][symb[j]] = atoi(p) ;
if (*p == '-') ++p ;
while (p && *p >= '0' && *p <= '9') ++p ;
while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
}
if (j != nsymb)
{ fprintf (stderr, "ERROR in readMatrix: bad line: %s\n", line) ;
fclose (fil) ;
return 0 ;
}
}
fclose (fil) ;
return 1 ;
}
/*********** standard conversion tables **************/
int dna2textConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', -2, 'C', -2, -2, -2, 'G', -2, -2, -2, -2, -2, -2, 'N', -2,
-2, -2, -2, -2, 'T', -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', -2, 'C', -2, -2, -2, 'G', -2, -2, -2, -2, -2, -2, 'N', -2,
-2, -2, -2, -2, 'T', -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int dna2textAmbig2NConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', 'N', 'C', 'N', -2, -2, 'G', 'N', -2, -2, 'N', -2, 'N', 'N', -2,
-2, -2, 'N', 'N', 'T', -2, 'N', 'N', -2, 'N', -2, -2, -2, -2, -2, -2,
-2, 'A', 'N', 'C', 'N', -2, -2, 'G', 'N', -2, -2, 'N', -2, 'N', 'N', -2,
-2, -2, 'N', 'N', 'T', -2, 'N', 'N', -2, 'N', -2, -2, -2, -2, -2, -2,
} ;
int dna2indexConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 0, -2, 1, -2, -2, -2, 2, -2, -2, -2, -2, -2, -2, 4, -2,
-2, -2, -2, -2, 3, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 0, -2, 1, -2, -2, -2, 2, -2, -2, -2, -2, -2, -2, 4, -2,
-2, -2, -2, -2, 3, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int dna2binaryConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 1, -2, 8, -2, -2, -2, 4, -2, -2, -2, -2, -2, -2, 15, -2,
-2, -2, -2, -2, 2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 1, -2, 8, -2, -2, -2, 4, -2, -2, -2, -2, -2, -2, 15, -2,
-2, -2, -2, -2, 2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int aa2textConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', 'X', 'C', 'D', 'E', 'F', 'G', 'H', 'I', -2, 'K', 'L', 'M', 'N', -2,
'P', 'Q', 'R', 'S', 'T', -2, 'V', 'W', 'X', 'Y', 'X', -2, -2, -2, -2, -2,
-2, 'A', 'X', 'C', 'D', 'E', 'F', 'G', 'H', 'I', -2, 'K', 'L', 'M', 'N', -2,
'P', 'Q', 'R', 'S', 'T', -2, 'V', 'W', 'X', 'Y', 'X', -2, -2, -2, -2, -2,
} ;
int aa2indexConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 0, 20, 1, 2, 3, 4, 5, 6, 7, -2, 8, 9, 10, 11, -2,
12, 13, 14, 15, 16, -2, 17, 18, 20, 19, 20, -2, -2, -2, -2, -2,
-2, 0, 20, 1, 2, 3, 4, 5, 6, 7, -2, 8, 9, 10, 11, -2,
12, 13, 14, 15, 16, -2, 17, 18, 20, 19, 20, -2, -2, -2, -2, -2,
} ;
int noConv[] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127
} ;
/**************** end of file ***************/