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sqio.c
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sqio.c
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/* SQUID - A C function library for biological sequence analysis
* Copyright (C) 1992-1995 Sean R. Eddy
*
* This source code is distributed under terms of the
* GNU General Public License. See the files COPYING
* and GNULICENSE for further details.
*
*/
/* File: sqio.c
* From: ureadseq.c in Don Gilbert's sequence i/o package
*
* Reads and writes nucleic/protein sequence in various
* formats. Data files may have multiple sequences.
*
* Heavily modified from READSEQ package
* Copyright (C) 1990 by D.G. Gilbert
* Biology Dept., Indiana University, Bloomington, IN 47405
* email: [email protected]
* Thanks Don!
*
* SRE: Modifications as noted. Fri Jul 3 09:44:54 1992
* Packaged for squid, Thu Oct 1 10:07:11 1992
* ANSI conversion in full swing, Mon Jul 12 12:22:21 1993
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#ifndef SEEK_SET
#include <unistd.h> /* may Sun Microsystems rot in hell */
#endif
#include "squid.h"
#ifdef MEMDEBUG
#include "dbmalloc.h"
#endif
/* Our hack for "sequential" access of sequences in
* interleaved-format alignment files (MSF, SELEX):
* static pointers at data for the entire alignment.
*/
static char **ali_aseqs;
static char **ali_rseqs;
static struct aliinfo_s ali_ainfo;
static int ali_num;
static int curridx;
#define kStartLength 500
static char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
static char *primenuc = "ACGTUN";
static char *protonly = "EFIPQZ";
/* static char stdsymbols[6] = "_.-*?"; */
static char allsymbols[32] = "_.-*?<>{}[]()!@#$%^&=+;:'|`~\"\\";
static char *seqsymbols = allsymbols;
/*
use general form of isseqchar -- all chars + symbols.
no formats except nbrf (?) use symbols in data area as
anything other than sequence chars.
(wrong. PIR-CODATA does. Remove /)
*/
void
FreeSequence(char *seq, SQINFO *sqinfo)
{
if (seq != NULL) free(seq);
if (sqinfo->flags & SQINFO_SS) free(sqinfo->ss);
if (sqinfo->flags & SQINFO_FREE) free(sqinfo->free);
if (sqinfo->flags & SQINFO_SA) free(sqinfo->sa);
}
int
SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag)
{
int len;
if (flag != SQINFO_FREE)
while (*sptr == ' ') sptr++; /* ignore leading whitespace */
switch (flag) {
case SQINFO_NAME:
if (*sptr != '-')
{
strncpy(sqinfo->name, sptr, 31);
sqinfo->name[31] = '\0';
sqinfo->flags |= SQINFO_NAME;
}
break;
case SQINFO_ID:
if (*sptr != '-')
{
strncpy(sqinfo->id, sptr, 31);
sqinfo->id[31] = '\0';
sqinfo->flags |= SQINFO_ID;
}
break;
case SQINFO_ACC:
if (*sptr != '-')
{
strncpy(sqinfo->acc, sptr, 31);
sqinfo->acc[31] = '\0';
sqinfo->flags |= SQINFO_ACC;
}
break;
case SQINFO_DESC:
if (*sptr != '-')
{
if (sqinfo->flags & SQINFO_DESC) /* append? */
{
len = strlen(sqinfo->desc);
if (len < 126) /* is there room? */
{
strncat(sqinfo->desc, " ", 127-len); len++;
strncat(sqinfo->desc, sptr, 127-len);
}
}
else /* else copy */
strncpy(sqinfo->desc, sptr, 127);
sqinfo->desc[127] = '\0';
sqinfo->flags |= SQINFO_DESC;
}
break;
case SQINFO_START:
if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
sqinfo->start = atoi(sptr);
if (sqinfo->start != 0) sqinfo->flags |= SQINFO_START;
break;
case SQINFO_STOP:
if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
sqinfo->stop = atoi(sptr);
if (sqinfo->stop != 0) sqinfo->flags |= SQINFO_STOP;
break;
case SQINFO_OLEN:
if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
sqinfo->olen = atoi(sptr);
if (sqinfo->olen != 0) sqinfo->flags |= SQINFO_OLEN;
break;
case SQINFO_WGT:
if (*sptr != '-')
{
if (!IsReal(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
sqinfo->weight = (float) atof(sptr);
sqinfo->flags |= SQINFO_WGT;
}
break;
case SQINFO_FREE:
if (sqinfo->flags & SQINFO_FREE) /* append? */
{
len = strlen(sqinfo->free) + strlen(sptr);
sqinfo->free = (char *) ReallocOrDie (sqinfo->free,
(len + 2) * sizeof(char));
strcat(sqinfo->free, sptr);
strcat(sqinfo->free, "\n");
}
else /* else copy */
{
len = strlen(sptr);
sqinfo->free = (char *) MallocOrDie ((len +2) * sizeof(char));
strcpy(sqinfo->free, sptr);
strcat(sqinfo->free, "\n");
sqinfo->flags |= SQINFO_FREE;
}
break;
default:
Die("Invalid flag %d to SetSeqinfoString()");
}
return 1;
}
void
SeqinfoCopy(SQINFO *sq1, SQINFO *sq2)
{
sq1->flags = sq2->flags;
if (sq2->flags & SQINFO_NAME) strcpy(sq1->name, sq2->name);
if (sq2->flags & SQINFO_ID) strcpy(sq1->id, sq2->id);
if (sq2->flags & SQINFO_ACC) strcpy(sq1->acc, sq2->acc);
if (sq2->flags & SQINFO_DESC) strcpy(sq1->desc, sq2->desc);
if (sq2->flags & SQINFO_LEN) sq1->len = sq2->len;
if (sq2->flags & SQINFO_START) sq1->start = sq2->start;
if (sq2->flags & SQINFO_STOP) sq1->stop = sq2->stop;
if (sq2->flags & SQINFO_OLEN) sq1->olen = sq2->olen;
if (sq2->flags & SQINFO_TYPE) sq1->type = sq2->type;
if (sq2->flags & SQINFO_WGT) sq1->weight = sq2->weight;
if (sq2->flags & SQINFO_SS) sq1->ss = strdup(sq2->ss);
if (sq2->flags & SQINFO_FREE) sq1->free = strdup(sq2->free);
if (sq2->flags & SQINFO_SA) sq1->sa = strdup(sq2->sa);
}
/* Function: ToDNA()
*
* Purpose: Convert a sequence to DNA.
* U --> T
*/
void
ToDNA(char *seq)
{
for (; *seq != '\0'; seq++)
{
if (*seq == 'U') *seq = 'T';
else if (*seq == 'u') *seq = 't';
}
}
/* Function: ToRNA()
*
* Purpose: Convert a sequence to RNA.
* T --> U
*/
void
ToRNA(char *seq)
{
for (; *seq != '\0'; seq++)
{
if (*seq == 'T') *seq = 'U';
else if (*seq == 't') *seq = 'u';
}
}
static int
isSeqChar(int c)
{
if (c > 127) return 0; /* IRIX 4.0 bug! isascii(255) returns TRUE */
return (isalpha(c) || strchr(seqsymbols,c));
}
static void
readline(FILE *f, char *s)
{
char *cp;
if (NULL == fgets(s, LINEBUFLEN, f))
*s = 0;
else {
cp = strchr(s, '\n');
if (cp != NULL) *cp = 0;
}
}
static void
getlines(struct ReadSeqVars *V)
{
readline(V->f, V->sbuffer);
}
/* Function: addseq()
*
* Purpose: Add a line of sequence to the growing string in V.
*/
static void
addseq(char *s, struct ReadSeqVars *V)
{
char *ptr;
while (*s != 0) {
if (isSeqChar((int) *s)) {
if (*s == '-' && V->dash_equals_n) *s = 'N';
if (V->seqlen >= V->maxseq) {
V->maxseq += kStartLength;
ptr = (char*) realloc(V->seq, V->maxseq+1);
if (ptr==NULL) {
squid_errno = SQERR_MEM;
return;
}
else V->seq = ptr;
}
V->seq[(V->seqlen)++] = *s;
}
s++;
}
}
static void
addstruc(char *s, struct ReadSeqVars *V)
{
char *sptr;
if (! (V->sqinfo->flags & SQINFO_SS))
{
if ((V->sqinfo->ss = (char *) malloc ((V->maxseq+1) * sizeof(char))) == NULL)
{ squid_errno = SQERR_MEM; return; }
V->sqinfo->flags |= SQINFO_SS;
sptr = V->sqinfo->ss;
}
else
{
if ((V->sqinfo->ss = (char *) realloc(V->sqinfo->ss, V->maxseq+1)) == NULL)
{ squid_errno = SQERR_MEM; return; }
sptr = V->sqinfo->ss;
while (*sptr != '\0') sptr++;
}
while (*s != 0)
{
if (isSeqChar((int)*s)) { *sptr = *s; sptr++; }
s++;
}
*sptr = '\0';
}
static void
readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
{
int addend = 0;
int done = 0;
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
getlines(V);
done = feof(V->f);
done |= (*endTest)(V->sbuffer, &addend);
if (addend || !done)
addseq(V->sbuffer, V);
} while (!done);
}
static int
endPIR(char *s, int *addend)
{
*addend = 0;
if ((strncmp(s, "///", 3) == 0) ||
(strncmp(s, "ENTRY", 5) == 0))
return 1;
else
return 0;
}
static void
readPIR(struct ReadSeqVars *V)
{
char *sptr;
/* load first line of entry */
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
getlines(V);
if (feof(V->f)) return;
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
{
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
getlines(V);
if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
{
if ((sptr = strtok(V->sbuffer+15, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
getlines(V); /* skip next line, coords */
readLoop(0, endPIR, V);
/* reading a real PIR-CODATA database file, we keep the source coords
*/
V->sqinfo->start = 1;
V->sqinfo->stop = V->seqlen;
V->sqinfo->olen = V->seqlen;
V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
getlines(V);
}
static int
endIG(char *s, int *addend)
{
*addend = 1; /* 1 or 2 occur in line w/ bases */
return((strchr(s,'1')!=NULL) || (strchr(s,'2')!=NULL));
}
static void
readIG(struct ReadSeqVars *V)
{
char *nm;
/* position past ';' comments */
do {
getlines(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
{
if ((nm = strtok(V->sbuffer, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
readLoop(0, endIG, V);
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
getlines(V);
}
static int
endStrider(char *s, int *addend)
{
*addend = 0;
return (strstr( s, "//") != NULL);
}
static void
readStrider(struct ReadSeqVars *V)
{
char *nm;
while ((!feof(V->f)) && (*V->sbuffer == ';'))
{
if (strncmp(V->sbuffer,"; DNA sequence", 14) == 0)
{
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
getlines(V);
}
if (! feof(V->f))
readLoop(1, endStrider, V);
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
getlines(V);
}
static int
endGB(char *s, int *addend)
{
*addend = 0;
return ((strstr(s,"//") != NULL) || (strstr(s,"LOCUS") == s));
}
static void
readGenBank(struct ReadSeqVars *V)
{
char *sptr;
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
getlines(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
in_definition = FALSE;
while (! feof(V->f))
{
getlines(V);
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
in_definition = TRUE;
}
else if (! feof(V->f) && strstr(V->sbuffer, "ACCESSION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
in_definition = FALSE;
}
else if (strncmp(V->sbuffer,"ORIGIN", 6) != 0)
{
if (in_definition)
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
else
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_FREE);
}
else
break;
}
readLoop(0, endGB, V);
/* reading a real GenBank database file, we keep the source coords
*/
V->sqinfo->start = 1;
V->sqinfo->stop = V->seqlen;
V->sqinfo->olen = V->seqlen;
V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
getlines(V);
/* SRE: V->s now holds "//", so sequential
reads are wedged: fixed Tue Jul 13 1993 */
while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
getlines(V);
}
static int
endNBRF(char *s, int *addend)
{
char *a;
if ((a = strchr(s, '*')) != NULL) { /* end of 1st seq */
/* "*" can be valid base symbol, drop it here */
*a = 0;
*addend = 1;
return(1);
}
else if (*s == '>') { /* start of next seq */
*addend = 0;
return(1);
}
else
return(0);
}
static void
readNBRF(struct ReadSeqVars *V)
{
char *sptr;
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
getlines(V); /*skip title-junk line*/
readLoop(0, endNBRF, V);
while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
getlines(V);
}
static int
endPearson(char *s, int *addend)
{
*addend = 0;
return(*s == '>');
}
static void
readPearson(struct ReadSeqVars *V)
{
char *sptr;
/* check for my special FASTA format */
if (strstr(V->sbuffer, "..") != NULL && strstr(V->sbuffer, "::") != NULL)
{
if ((sptr = strtok(V->sbuffer+1, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
if ((sptr = strtok(NULL, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_WGT);
if ((sptr = strtok(NULL, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
if ((sptr = strtok(NULL, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
if ((sptr = strtok(NULL, ".")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_START);
if ((sptr = strtok(NULL, ".:")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_STOP);
if ((sptr = strtok(NULL, ":\t\n ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_OLEN);
if ((sptr = strtok(NULL, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
}
else /* else we're normal FASTA format */
{
if ((sptr = strtok(V->sbuffer+1, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
if ((sptr = strtok(NULL, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
}
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
getlines(V);
}
static int
endEMBL(char *s, int *addend)
{
*addend = 0;
return ((strstr(s,"//") != NULL) || (strstr(s,"ID ") == s));
}
static void
readEMBL(struct ReadSeqVars *V)
{
char *sptr;
/* make sure we have first line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
getlines(V);
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
{
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
getlines(V);
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
else if (!feof(V->f) && strstr(V->sbuffer, "DE ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
}
} while (! feof(V->f) && strncmp(V->sbuffer,"SQ",2) != 0);
readLoop(0, endEMBL, V);
/* reading a real EMBL database file, we keep the source coords
*/
V->sqinfo->start = 1;
V->sqinfo->stop = V->seqlen;
V->sqinfo->olen = V->seqlen;
V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
getlines(V);
}
static int
endZuker(char *s, int *addend)
{
*addend = 0;
return( *s == '(' );
}
static void
readZuker(struct ReadSeqVars *V)
{
char *sptr;
getlines(V); /*s == "seqLen seqid string..."*/
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
if ((sptr = strtok(NULL, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
getlines(V);
}
static void
readUWGCG(struct ReadSeqVars *V)
{
char *si;
char *sptr;
int done;
V->seqlen = 0;
/*writeseq: " %s Length: %d (today) Check: %d ..\n" */
/*drop above or ".." from id*/
if ((si = strstr(V->sbuffer," Length: ")) != NULL) *si = 0;
else if ((si = strstr(V->sbuffer,"..")) != NULL) *si = 0;
if ((sptr = strtok(V->sbuffer, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
do {
done = feof(V->f);
getlines(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
static void
readSquid(struct ReadSeqVars *V)
{
char *sptr;
int dostruc = FALSE;
while (strncmp(V->sbuffer, "NAM ", 4) != 0) getlines(V);
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
while (1)
{
getlines(V);
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
if (strncmp(V->sbuffer, "SRC ", 4) == 0)
{
if ((sptr = strtok(V->sbuffer+4, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
if ((sptr = strtok(NULL, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
if ((sptr = strtok(NULL, ".")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_START);
if ((sptr = strtok(NULL, ".:")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_STOP);
if ((sptr = strtok(NULL, ": \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_OLEN);
}
else if (strncmp(V->sbuffer, "DES ", 4) == 0)
{
if ((sptr = strtok(V->sbuffer+4, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
}
else if (strncmp(V->sbuffer,"SEQ", 3) == 0)
break;
}
if (strstr(V->sbuffer, "+SS") != NULL) dostruc = TRUE;
V->seqlen = 0;
while (1)
{
/* sequence line */
getlines(V);
if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
break;
addseq(V->sbuffer, V);
/* structure line */
if (dostruc)
{
getlines(V);
if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
addstruc(V->sbuffer, V);
}
}
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
getlines(V);
}
/* Function: SeqfileOpen()
*
* Purpose : Open a sequence database file and prepare for reading
* sequentially.
*
* Args: filename - name of file to open
* format - format of file
* env - environment variable for path (e.g. BLASTDB)
*
* Returns opened SQFILE ptr, or NULL on failure.
*/
SQFILE *
SeqfileOpen(char *filename, int format, char *env)
{
SQFILE *dbfp;
if ((dbfp = (SQFILE *) malloc (sizeof(SQFILE))) == NULL)
{ squid_errno = SQERR_MEM; return NULL; }
if ((dbfp->f = fopen(filename, "r")) == NULL &&
(dbfp->f = EnvFileOpen(filename, env)) == NULL)
{ squid_errno = SQERR_NOFILE; return NULL; }
/* If it's a SELEX- or MSF-formatted alignment file, we
* hack a way to fake sequential access: read the whole
* alignment into a static at once. Relies on the prediction
* that these files will always be relatively small, unlike
* GenBank or EMBL databases.
*/
/* Note (Tue Aug 30 11:57:19 1994): This cause a bug:
* ReadSeq() is not reentrant for alignment files.
*/
if (format == kSelex || format == kMSF)
{
if (! ReadAlignment(filename, format, &ali_aseqs, &ali_num, &ali_ainfo))
return NULL;
if (! DealignAseqs(ali_aseqs, ali_num, &ali_rseqs))
return NULL;
curridx = 0;
}
/* Load the first line.
*/
getlines(dbfp);
return dbfp;
}
/* Function: SeqfilePosition()
*
* Purpose: Move to a particular offset in a seqfile.
* Will not work on interleaved files (SELEX, MSF).
*/
void
SeqfilePosition(SQFILE *sqfp, long offset)
{
fseek(sqfp->f, offset, SEEK_SET);
getlines(sqfp);
}
void
SeqfileClose(SQFILE *sqfp)
{
fclose(sqfp->f);
free(sqfp);
}
/* Function: ReadSeq()
*
* Purpose: Read next sequence from an open database file.
* Return the sequence and associated info.
*
* Args: fp - open sequence database file pointer
* format - format of the file (previously determined
* by call to SeqfileFormat())
* ret_seq - RETURN: sequence
* sqinfo - RETURN: filled in w/ other information
*
* Return: 1 on success, 0 on failure.
* ret_seq and some field of sqinfo are allocated here,
* The preferred call mechanism to properly free the memory is:
*
* SQINFO sqinfo;
* char *seq;
*
* ReadSeq(fp, format, &seq, &sqinfo);
* ... do something...
* FreeSequence(seq, &sqinfo);
*/
int
ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
{
int gotuw;
squid_errno = SQERR_OK;
if (format < kMinFormat || format > kMaxFormat)
{
squid_errno = SQERR_FORMAT;
*ret_seq = NULL;
return 0;
}
/* Here's the hack for accessing sequences from
* the multiple sequence alignment formats
*/
if (format == kMSF || format == kSelex)
{
if (curridx >= ali_num)
{ /* none left; free static ptrs */
FreeAlignment(ali_aseqs, ali_num, &ali_ainfo);
free(ali_rseqs); /* only free rseqs pointer array */
return 0;
}
SeqinfoCopy(sqinfo, &(ali_ainfo.sqinfo[curridx]));
*ret_seq = ali_rseqs[curridx];
curridx++;
return 1;
}
else
{
if (feof(V->f)) return 0;
V->seq = (char*) calloc (kStartLength+1, sizeof(char));
V->maxseq = kStartLength;
V->seqlen = 0;
V->sqinfo = sqinfo;
V->sqinfo->flags = 0;
V->dash_equals_n = (format == kEMBL) ? TRUE : FALSE;
switch (format) {
case kIG : readIG(V); break;
case kStrider: readStrider(V); break;
case kGenBank: readGenBank(V); break;
case kNBRF : readNBRF(V); break;
case kPearson: readPearson(V); break;
case kEMBL : readEMBL(V); break;
case kZuker : readZuker(V); break;
case kPIR : readPIR(V); break;
case kSquid : readSquid(V); break;
case kGCG:
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
getlines(V);
} while (! feof(V->f));
break;
case kIdraw: /* SRE: no attempt to read idraw postscript */
default:
squid_errno = SQERR_FORMAT;
free(V->seq);
return 0;
}
V->seq[V->seqlen] = 0; /* stick a string terminator on it */
}
/* Cleanup
*/
sqinfo->len = V->seqlen;
sqinfo->flags |= SQINFO_LEN;
*ret_seq = V->seq;
if (squid_errno == SQERR_OK) return 1; else return 0;
}
/* Function: SeqfileFormat()
*
* Purpose: Determine format of seqfile, and return it
* through ret_format. From Gilbert's seqFileFormat().
*
* Return: 1 on success, 0 on failure.
*/
int
SeqfileFormat(char *filename, int *ret_format, char *env)
{
int foundIG = 0;
int foundStrider = 0;
int foundGB = 0;
int foundEMBL = 0;
int foundNBRF = 0;
int foundPearson = 0;
int foundZuker = 0;
int gotPIR = 0;
int gotSquid = 0;
int gotuw = 0;
int done = 0;
int gotMSF = 0;
int format = kUnknown;
int nlines= 0, dnalines= 0;
int splen = 0;
char sp[LINEBUFLEN];
FILE *fseq;
#define ReadOneLine(sp) \
{ done |= (feof(fseq)); \
readline( fseq, sp); \
if (!done) { splen = (int) strlen(sp); ++nlines; } }
if ((fseq = fopen(filename, "r")) == NULL &&
(fseq = EnvFileOpen(filename, env)) == NULL)
{ squid_errno = SQERR_NOFILE; return 0; }
/* Look at a line at a time
*/
while ( !done ) {
ReadOneLine(sp);
if (sp==NULL || *sp==0)
; /* nada */
/* high probability identities: */
else if (strstr(sp, "MSF:") != NULL &&
strstr(sp, "Type:") != NULL &&
strstr(sp, "Check:") != NULL)
gotMSF = 1;
else if (strstr(sp,"Check:") != NULL)
gotuw= 1;
else if ((strncmp(sp, "///", 3) == 0) ||
(strncmp(sp, "ENTRY ", 6) == 0))
gotPIR = 1;
else if (strncmp(sp, "++", 2) == 0 ||
strncmp(sp, "NAM ", 4) == 0)
gotSquid = 1;
/* uncertain identities: */
else if (*sp ==';') {
if (strstr(sp,"Strider") !=NULL) foundStrider= 1;
else foundIG= 1;