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readseq/ureadseq.c

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/* File: ureadseq.c
*
* Reads and writes nucleic/protein sequence in various
* formats. Data files may have multiple sequences.
*
* Copyright 1990 by d.g.gilbert
* biology dept., indiana university, bloomington, in 47405
* e-mail: gilbertd@bio.indiana.edu
*
* This program may be freely copied and used by anyone.
* Developers are encourged to incorporate parts in their
* programs, rather than devise their own private sequence
* format.
*
* This should compile and run with any ANSI C compiler.
*
*/
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define UREADSEQ_G
#include "ureadseq.h"
#pragma segment ureadseq
int Strcasecmp(const char *a, const char *b) /* from Nlm_StrICmp */
{
int diff, done;
if (a == b) return 0;
done = 0;
while (!done) {
diff = to_upper(*a) - to_upper(*b);
if (diff) return diff;
if (*a == '\0')
done = 1;
else {
a++;
b++;
}
}
return 0;
}
int Strncasecmp(const char *a, const char *b, long maxn) /* from Nlm_StrNICmp */
{
int diff, done;
if (a == b) return 0;
done = 0;
while (!done) {
diff = to_upper(*a) - to_upper(*b);
if (diff) return diff;
if (*a == '\0')
done = 1;
else {
a++;
b++;
maxn--;
if (!maxn) done = 1;
}
}
return 0;
}
#ifndef Local
#define Local static /* local functions */
#endif
#define kStartLength 500
const char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
const char *primenuc = "ACGTU";
const char *protonly = "EFIPQZ";
const char kNocountsymbols[5] = "_.-?";
const char stdsymbols[6] = "_.-*?";
const char allsymbols[32] = "_.-*?<>{}[]()!@#$%^&=+;:'/|`~\"\\";
static const char *seqsymbols = allsymbols;
const char nummask[11] = "0123456789";
const char nonummask[11] = "~!@#$%^&*(";
/*
use general form of isseqchar -- all chars + symbols.
no formats except nbrf (?) use symbols in data area as
anything other than sequence chars.
*/
/* Local variables for readSeq: */
struct ReadSeqVars {
short choice, err, nseq;
long seqlen, maxseq, seqlencount;
short topnseq;
long topseqlen;
const char *fname;
char *seq, *seqid, matchchar;
boolean allDone, done, filestart, addit;
FILE *f;
long linestart;
char s[256], *sp;
int (*isseqchar)();
/* int (*isseqchar)(int c); << sgi cc hates (int c) */
};
int isSeqChar(int c) { return (isalpha(c) || strchr(seqsymbols, c)); }
int isSeqNumChar(int c) { return (isalnum(c) || strchr(seqsymbols, c)); }
int isAnyChar(int c) { return isascii(c); /* wrap in case isascii is macro */ }
Local void readline(FILE *f, char *s, long *linestart)
{
char *cp;
*linestart = ftell(f);
if (NULL == fgets(s, 256, f))
*s = 0;
else {
cp = strchr(s, '\n');
if (cp != NULL) *cp = 0;
}
}
Local void cgetline(struct ReadSeqVars *V)
{
readline(V->f, V->s, &V->linestart);
}
Local void ungetline(struct ReadSeqVars *V) { fseek(V->f, V->linestart, 0); }
Local void addseq(char *s, struct ReadSeqVars *V)
{
char *ptr;
if (V->addit)
while (*s != 0) {
if ((V->isseqchar)(*s)) {
if (V->seqlen >= V->maxseq) {
V->maxseq += kStartLength;
ptr = (char *)realloc(V->seq,
V->maxseq + 1);
if (ptr == NULL) {
V->err = eMemFull;
return;
}
else
V->seq = ptr;
}
V->seq[(V->seqlen)++] = *s;
}
s++;
}
}
Local void countseq(char *s, struct ReadSeqVars *V)
/* this must count all valid seq chars, for some formats (paup-sequential) even
if we are skipping seq... */
{
while (*s != 0) {
if ((V->isseqchar)(*s)) {
(V->seqlencount)++;
}
s++;
}
}
Local void addinfo(char *s, struct ReadSeqVars *V)
{
char s2[256], *si;
boolean saveadd;
si = s2;
while (*s == ' ') s++;
sprintf(si, " %d) %s\n", V->nseq, s);
saveadd = V->addit;
V->addit = true;
V->isseqchar = isAnyChar;
addseq(si, V);
V->addit = saveadd;
V->isseqchar = isSeqChar;
}
Local void readLoop(short margin, boolean addfirst,
boolean (*endTest)(boolean *addend, boolean *ungetend,
struct ReadSeqVars *V),
struct ReadSeqVars *V)
{
boolean addend = false;
boolean ungetend = false;
V->nseq++;
if (V->choice == kListSequences)
V->addit = false;
else
V->addit = (V->nseq == V->choice);
if (V->addit) V->seqlen = 0;
if (addfirst) addseq(V->s, V);
do {
cgetline(V);
V->done = feof(V->f);
V->done |= (*endTest)(&addend, &ungetend, V);
if (V->addit && (addend || !V->done) &&
(strlen(V->s) > margin)) {
addseq((V->s) + margin, V);
}
} while (!V->done);
if (V->choice == kListSequences)
addinfo(V->seqid, V);
else {
V->allDone = (V->nseq >= V->choice);
if (V->allDone && ungetend) ungetline(V);
}
}
Local boolean endIG(boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
{
*addend = true; /* 1 or 2 occur in line w/ bases */
*ungetend = false;
return ((strchr(V->s, '1') != NULL) || (strchr(V->s, '2') != NULL));
}
Local void readIG(struct ReadSeqVars *V)
{
/* 18Aug92: new IG format -- ^L between sequences in place of ";" */
char *si;
while (!V->allDone) {
do {
cgetline(V);
for (si = V->s; *si != 0 && *si < ' '; si++)
*si = ' '; /* drop controls */
if (*si == 0) *V->s = 0; /* chop line to empty */
} while (!(feof(V->f) || ((*V->s != 0) && (*V->s != ';'))));
if (feof(V->f))
V->allDone = true;
else {
strcpy(V->seqid, V->s);
readLoop(0, false, endIG, V);
}
}
}
Local boolean endStrider(boolean *addend, boolean *ungetend,
struct ReadSeqVars *V)
{
*addend = false;
*ungetend = false;
return (strstr(V->s, "//") != NULL);
}
Local void readStrider(struct ReadSeqVars *V)
{ /* ? only 1 seq/file ? */
while (!V->allDone) {
cgetline(V);
if (strstr(V->s, "; DNA sequence ") == V->s)
strcpy(V->seqid, (V->s) + 16);
else
strcpy(V->seqid, (V->s) + 1);
while ((!feof(V->f)) && (*V->s == ';')) {
cgetline(V);
}
if (feof(V->f))
V->allDone = true;
else
readLoop(0, true, endStrider, V);
}
}
Local boolean endPIR(boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
{
*addend = false;
*ungetend = (strstr(V->s, "ENTRY") == V->s);
return ((strstr(V->s, "///") != NULL) || *ungetend);
}
Local void readPIR(struct ReadSeqVars *V)
{ /*PIR -- many seqs/file */
while (!V->allDone) {
while (!(feof(V->f) || strstr(V->s, "ENTRY") ||
strstr(V->s, "SEQUENCE")))
cgetline(V);
strcpy(V->seqid, (V->s) + 16);
while (!(feof(V->f) || strstr(V->s, "SEQUENCE") == V->s))
cgetline(V);
readLoop(0, false, endPIR, V);
if (!V->allDone) {
while (!(
feof(V->f) ||
((*V->s != 0) && (strstr(V->s, "ENTRY") == V->s))))
cgetline(V);
}
if (feof(V->f)) V->allDone = true;
}
}
Local boolean endGB(boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
{
*addend = false;
*ungetend = (strstr(V->s, "LOCUS") == V->s);
return ((strstr(V->s, "//") != NULL) || *ungetend);
}
Local void readGenBank(struct ReadSeqVars *V)
{ /*GenBank -- many seqs/file */
while (!V->allDone) {
strcpy(V->seqid, (V->s) + 12);
while (!(feof(V->f) || strstr(V->s, "ORIGIN") == V->s))
cgetline(V);
readLoop(0, false, endGB, V);
if (!V->allDone) {
while (!(
feof(V->f) ||
((*V->s != 0) && (strstr(V->s, "LOCUS") == V->s))))
cgetline(V);
}
if (feof(V->f)) V->allDone = true;
}
}
Local boolean endNBRF(boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
{
char *a;
if ((a = strchr(V->s, '*')) != NULL) { /* end of 1st seq */
/* "*" can be valid base symbol, drop it here */
*a = 0;
*addend = true;
*ungetend = false;
return (true);
}
else if (*V->s == '>') { /* start of next seq */
*addend = false;
*ungetend = true;
return (true);
}
else
return (false);
}
Local void readNBRF(struct ReadSeqVars *V)
{
while (!V->allDone) {
strcpy(V->seqid, (V->s) + 4);
cgetline(V); /*skip title-junk line*/
readLoop(0, false, endNBRF, V);
if (!V->allDone) {
while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
cgetline(V);
}
if (feof(V->f)) V->allDone = true;
}
}
Local boolean endPearson(boolean *addend, boolean *ungetend,
struct ReadSeqVars *V)
{
*addend = false;
*ungetend = true;
return (*V->s == '>');
}
Local void readPearson(struct ReadSeqVars *V)
{
while (!V->allDone) {
strcpy(V->seqid, (V->s) + 1);
readLoop(0, false, endPearson, V);
if (!V->allDone) {
while (
!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
cgetline(V);
}
if (feof(V->f)) V->allDone = true;
}
}
Local boolean endEMBL(boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
{
*addend = false;
*ungetend = (strstr(V->s, "ID ") == V->s);
return ((strstr(V->s, "//") != NULL) || *ungetend);
}
Local void readEMBL(struct ReadSeqVars *V)
{
while (!V->allDone) {
strcpy(V->seqid, (V->s) + 5);
do {
cgetline(V);
} while (!(feof(V->f) | (strstr(V->s, "SQ ") == V->s)));
readLoop(0, false, endEMBL, V);
if (!V->allDone) {
while (
!(feof(V->f) | ((*V->s != '\0') &
(strstr(V->s, "ID ") == V->s))))
cgetline(V);
}
if (feof(V->f)) V->allDone = true;
}
}
Local boolean endZuker(boolean *addend, boolean *ungetend,
struct ReadSeqVars *V)
{
*addend = false;
*ungetend = true;
return (*V->s == '(');
}
Local void readZuker(struct ReadSeqVars *V)
{
/*! 1st string is Zuker's Fortran format */
while (!V->allDone) {
cgetline(V); /*s == "seqLen seqid string..."*/
strcpy(V->seqid, (V->s) + 6);
readLoop(0, false, endZuker, V);
if (!V->allDone) {
while (
!(feof(V->f) | ((*V->s != '\0') & (*V->s == '('))))
cgetline(V);
}
if (feof(V->f)) V->allDone = true;
}
}
Local boolean endFitch(boolean *addend, boolean *ungetend,
struct ReadSeqVars *V)
{
/* this is a somewhat shaky end,
1st char of line is non-blank for seq. title
*/
*addend = false;
*ungetend = true;
return (*V->s != ' ');
}
Local void readFitch(struct ReadSeqVars *V)
{
boolean first;
first = true;
while (!V->allDone) {
if (!first) strcpy(V->seqid, V->s);
readLoop(0, first, endFitch, V);
if (feof(V->f)) V->allDone = true;
first = false;
}
}
Local void readPlain(struct ReadSeqVars *V)
{
V->nseq++;
V->addit = (V->choice > 0);
if (V->addit) V->seqlen = 0;
addseq(V->seqid, V); /*from above..*/
if (V->fname != NULL)
sprintf(V->seqid, "%s [Unknown form]", V->fname);
else
sprintf(V->seqid, " [Unknown form]");
do {
addseq(V->s, V);
V->done = feof(V->f);
cgetline(V);
} while (!V->done);
if (V->choice == kListSequences) addinfo(V->seqid, V);
V->allDone = true;
}
Local void readUWGCG(struct ReadSeqVars *V)
{
/*
10nov91: Reading GCG files casued duplication of last line when
EOF followed that line !!!
fix: cgetline now sets *V->s = 0
*/
char *si;
V->nseq++;
V->addit = (V->choice > 0);
if (V->addit) V->seqlen = 0;
strcpy(V->seqid, V->s);
/*writeseq: " %s Length: %d (today) Check: %d ..\n" */
/*drop above or ".." from id*/
if (si = strstr(V->seqid, " Length: "))
*si = 0;
else if (si = strstr(V->seqid, ".."))
*si = 0;
do {
V->done = feof(V->f);
cgetline(V);
if (!V->done) addseq((V->s), V);
} while (!V->done);
if (V->choice == kListSequences) addinfo(V->seqid, V);
V->allDone = true;
}
Local void readOlsen(struct ReadSeqVars *V)
{ /* G. Olsen /print output from multiple sequence editor */
char *si, *sj, *sk, *sm, sid[40], snum[20];
boolean indata = false;
int snumlen;
V->addit = (V->choice > 0);
if (V->addit) V->seqlen = 0;
rewind(V->f);
V->nseq = 0;
do {
cgetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s))
break;
else if (indata) {
if ((si = strstr(V->s, sid))
/* && (strstr(V->s, snum) == si - snumlen - 1) ) {
*/
&& (sm = strstr(V->s, snum)) &&
(sm < si - snumlen)) {
/* Spaces are valid alignment data !! */
/* 17Oct91: Error, the left margin is 21 not 22!
*/
/* dropped some nucs up to now -- my example
* file was right shifted ! */
/* variable right id margin, drop id-2 spaces at
* end */
/*
VMS CC COMPILER (VAXC031) mess up:
-- Index of 21 is chopping 1st nuc on VMS
systems Only! Byte-for-byte same ame
rnasep.olsen sequence file !
*/
/* si = (V->s)+21; < was this before VMS CC
* wasted my time */
si += 10; /* use strstr index plus offset to
outfox VMS CC bug */
if (sk = strstr(si, sid)) *(sk - 2) = 0;
for (sk = si; *sk != 0; sk++) {
if (*sk == ' ') *sk = '.';
/* 18aug92: !! some olsen masks are
* NUMBERS !! which addseq eats */
else if (isdigit(*sk))
*sk = nonummask[*sk - '0'];
}
addseq(si, V);
}
}
else if (sk = strstr(V->s, "): ")) { /* seq info header line */
/* 18aug92: correct for diff seqs w/ same name -- use
* number, e.g. */
/* 3 (Agr.tume): agrobacterium.prna 18-JUN-1987
* 16:12 */
/* 328 (Agr.tume): agrobacterium.prna XYZ 19-DEC-1992
*/
(V->nseq)++;
si = 1 + strchr(V->s, '(');
*sk = ' ';
if (V->choice == kListSequences)
addinfo(si, V);
else if (V->nseq == V->choice) {
strcpy(V->seqid, si);
sj = strchr(V->seqid, ':');
while (*(--sj) == ' ')
;
while (--sj != V->seqid) {
if (*sj == ' ') *sj = '_';
}
*sk = 0;
while (*(--sk) == ' ') *sk = 0;
strcpy(sid, si);
si = V->s;
while ((*si <= ' ') && (*si != 0)) si++;
snumlen = 0;
while (si[snumlen] > ' ' && snumlen < 20) {
snum[snumlen] = si[snumlen];
snumlen++;
}
snum[snumlen] = 0;
}
}
else if (strstr(V->s, "identity: Data:")) {
indata = true;
if (V->choice == kListSequences) V->done = true;
}
} while (!V->done);
V->allDone = true;
} /*readOlsen*/
Local void readMSF(struct ReadSeqVars *V)
{ /* gcg's MSF, mult. sequence format, interleaved ! */
char *si, *sj, sid[128];
boolean indata = false;
int atseq = 0, iline = 0;
V->addit = (V->choice > 0);
if (V->addit) V->seqlen = 0;
rewind(V->f);
V->nseq = 0;
do {
cgetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s))
break;
else if (indata) {
/*somename ...gpvedai .......t.. aaigr..vad tvgtgptnse
* aipaltaaet */
/* E gvenae.kgv tentna.tad fvaqpvylpe .nqt......
* kv.affynrs */
si = V->s;
skipwhitespace(si);
/* for (sj= si; isalnum(*sj); sj++) ; bug -- cdelwiche
* uses "-", "_" and others in names*/
for (sj = si; *sj > ' '; sj++)
;
*sj = 0;
if (*si) {
if ((0 == strcmp(si, sid))) {
addseq(sj + 1, V);
}
iline++;
}
}
else if (NULL !=
(si = strstr(V->s,
"Name: "))) { /* seq info header line */
/* Name: somename Len: 100 Check: 7009
* Weight: 1.00 */
(V->nseq)++;
si += 6;
if (V->choice == kListSequences)
addinfo(si, V);
else if (V->nseq == V->choice) {
strcpy(V->seqid, si);
si = V->seqid;
skipwhitespace(si);
/* for (sj= si; isalnum(*sj); sj++) ; -- bug */
for (sj = si; *sj > ' '; sj++)
;
*sj = 0;
strcpy(sid, si);
}
}
else if (strstr(V->s, "//") /*== V->s*/) {
indata = true;
iline = 0;
if (V->choice == kListSequences) V->done = true;
}
} while (!V->done);
V->allDone = true;
} /*readMSF*/
Local void readPAUPinterleaved(struct ReadSeqVars *V)
{ /* PAUP mult. sequence format, interleaved or sequential! */
char *si, *sj, *send, sid[40], sid1[40], saveseq[255];
boolean first = true, indata = false, domatch;
int atseq = 0, iline = 0, ifmc, saveseqlen = 0;
#define fixmatchchar(s) \
{ \
for (ifmc = 0; ifmc < saveseqlen; ifmc++) \
if (s[ifmc] == V->matchchar) s[ifmc] = saveseq[ifmc]; \
}
V->addit = (V->choice > 0);
V->seqlencount = 0;
if (V->addit) V->seqlen = 0;
/* rewind(V->f); V->nseq= 0; << do in caller !*/
indata = true; /* call here after we find "matrix" */
domatch = (V->matchchar > 0);
do {
cgetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s))
break;
else if (indata) {
/* [ 1 1 1
* ]*/
/* human aagcttcaccggcgcagtca ttctcataatcgcccacggR
* cttacatcct*/
/* chimp ................a.t. .c.................a
* ..........*/
/* !! need to correct for V->matchchar */
si = V->s;
skipwhitespace(si);
if (strchr(si, ';')) indata = false;
if (isalnum(*si)) {
/* valid data line starts w/ a left-justified
* seq name in columns [0..8] */
if (first) {
(V->nseq)++;
if (V->nseq >= V->topnseq)
first = false;
for (sj = si; isalnum(*sj); sj++)
;
send = sj;
skipwhitespace(sj);
if (V->choice == kListSequences) {
*send = 0;
addinfo(si, V);
}
else if (V->nseq == V->choice) {
if (domatch) {
if (V->nseq == 1) {
strcpy(saveseq,
sj);
saveseqlen =
strlen(
saveseq);
}
else
fixmatchchar(
sj);
}
addseq(sj, V);
*send = 0;
strcpy(V->seqid, si);
strcpy(sid, si);
if (V->nseq == 1)
strcpy(sid1, sid);
}
}
else if ((strstr(si, sid) == si)) {
while (isalnum(*si)) si++;
skipwhitespace(si);
if (domatch) {
if (V->nseq == 1) {
strcpy(saveseq, si);
saveseqlen =
strlen(saveseq);
}
else
fixmatchchar(si);
}
addseq(si, V);
}
else if (domatch && (strstr(si, sid1) == si)) {
strcpy(saveseq, si);
saveseqlen = strlen(saveseq);
}
iline++;
}
}
else if (strstr(V->s, "matrix")) {
indata = true;
iline = 0;
if (V->choice == kListSequences) V->done = true;
}
} while (!V->done);
V->allDone = true;
} /*readPAUPinterleaved*/
Local void readPAUPsequential(struct ReadSeqVars *V)
{ /* PAUP mult. sequence format, interleaved or sequential! */
char *si, *sj;
boolean atname = true, indata = false;
V->addit = (V->choice > 0);
if (V->addit) V->seqlen = 0;
V->seqlencount = 0;
/* rewind(V->f); V->nseq= 0; << do in caller !*/
indata = true; /* call here after we find "matrix" */
do {
cgetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s))
break;
else if (indata) {
/* [ 1 1 1
* ]*/
/* human aagcttcaccggcgcagtca ttctcataatcgcccacggR
* cttacatcct*/
/* aagcttcaccggcgcagtca ttctcataatcgcccacggR
* cttacatcct*/
/* chimp ................a.t. .c.................a
* ..........*/
/* ................a.t. .c.................a
* ..........*/
si = V->s;
skipwhitespace(si);
if (strchr(si, ';')) indata = false;
if (isalnum(*si)) {
/* valid data line starts w/ a left-justified
* seq name in columns [0..8] */
if (atname) {
(V->nseq)++;
V->seqlencount = 0;
atname = false;
sj = si + 1;
while (isalnum(*sj)) sj++;
if (V->choice == kListSequences) {
/* !! we must count bases to
* know when topseqlen is
* reached ! */
countseq(sj, V);
if (V->seqlencount >=
V->topseqlen)
atname = true;
*sj = 0;
addinfo(si, V);
}
else if (V->nseq == V->choice) {
addseq(sj, V);
V->seqlencount = V->seqlen;
if (V->seqlencount >=
V->topseqlen)
atname = true;
*sj = 0;
strcpy(V->seqid, si);
}
else {
countseq(sj, V);
if (V->seqlencount >=
V->topseqlen)
atname = true;
}
}
else if (V->nseq == V->choice) {
addseq(V->s, V);
V->seqlencount = V->seqlen;
if (V->seqlencount >= V->topseqlen)
atname = true;
}
else {
countseq(V->s, V);
if (V->seqlencount >= V->topseqlen)
atname = true;
}
}
}
else if (strstr(V->s, "matrix")) {
indata = true;
atname = true;
if (V->choice == kListSequences) V->done = true;
}
} while (!V->done);
V->allDone = true;
} /*readPAUPsequential*/
Local void readPhylipInterleaved(struct ReadSeqVars *V)
{
char *si, *sj;
boolean first = true;
int iline = 0;
V->addit = (V->choice > 0);
if (V->addit) V->seqlen = 0;
V->seqlencount = 0;
/* sscanf( V->s, "%d%d", &V->topnseq, &V->topseqlen); << topnseq == 0
* !!! bad scan !! */
si = V->s;
skipwhitespace(si);
V->topnseq = atoi(si);
while (isdigit(*si)) si++;
skipwhitespace(si);
V->topseqlen = atol(si);
/* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq,
* V->topseqlen); */
do {
cgetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
si = V->s;
skipwhitespace(si);
if (*si != 0) {
if (first) { /* collect seq names + seq, as
fprintf(outf,"%-10s ",seqname); */
(V->nseq)++;
if (V->nseq >= V->topnseq) first = false;
sj = V->s + 10; /* past name, start of data */
if (V->choice == kListSequences) {
*sj = 0;
addinfo(si, V);
}
else if (V->nseq == V->choice) {
addseq(sj, V);
*sj = 0;
strcpy(V->seqid, si);
}
}
else if (iline % V->nseq == V->choice - 1) {
addseq(si, V);
}
iline++;
}
} while (!V->done);
V->allDone = true;
} /*readPhylipInterleaved*/
Local boolean endPhylipSequential(boolean *addend, boolean *ungetend,
struct ReadSeqVars *V)
{
*addend = false;
*ungetend = false;
countseq(V->s, V);
return V->seqlencount >= V->topseqlen;
}
Local void readPhylipSequential(struct ReadSeqVars *V)
{
short i;
char *si;
/* sscanf( V->s, "%d%d", &V->topnseq, &V->topseqlen); < ? bad sscan ? */
si = V->s;
skipwhitespace(si);
V->topnseq = atoi(si);
while (isdigit(*si)) si++;
skipwhitespace(si);
V->topseqlen = atol(si);
cgetline(V);
while (!V->allDone) {
V->seqlencount = 0;
strncpy(V->seqid, (V->s), 10);
V->seqid[10] = 0;
for (i = 0; i < 10 && V->s[i]; i++) V->s[i] = ' ';
readLoop(0, true, endPhylipSequential, V);
if (feof(V->f)) V->allDone = true;
}
}
Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
const short format_)
{
#define tolowerstr(s) \
{ \
long Itlwr, Ntlwr = strlen(s); \
for (Itlwr = 0; Itlwr < Ntlwr; Itlwr++) \
s[Itlwr] = to_lower(s[Itlwr]); \
}
boolean gotuw;
long l;
V->linestart = 0;
V->matchchar = 0;
if (V->f == NULL)
V->err = eFileNotFound;
else {
for (l = skiplines_; l > 0; l--) cgetline(V);
do {
cgetline(V);
for (l = strlen(V->s); (l > 0) && (V->s[l] == ' '); l--)
;
} while ((l == 0) && !feof(V->f));
if (feof(V->f))
V->err = eNoData;
else
switch (format_) {
case kPlain:
readPlain(V);
break;
case kIG:
readIG(V);
break;
case kStrider:
readStrider(V);
break;
case kGenBank:
readGenBank(V);
break;
case kPIR:
readPIR(V);
break;
case kNBRF:
readNBRF(V);
break;
case kPearson:
readPearson(V);
break;
case kEMBL:
readEMBL(V);
break;
case kZuker:
readZuker(V);
break;
case kOlsen:
readOlsen(V);
break;
case kMSF:
readMSF(V);
break;
case kPAUP: {
boolean done = false;
boolean interleaved = false;
char *cp;
/* rewind(V->f); V->nseq= 0; ?? assume
* it is at top ?? skiplines ... */
while (!done) {
cgetline(V);
tolowerstr(V->s);
if (strstr(V->s, "matrix"))
done = true;
if (strstr(V->s, "interleav"))
interleaved = true;
if (NULL !=
(cp =
strstr(V->s, "ntax=")))
V->topnseq =
atoi(cp + 5);
if (NULL !=
(cp = strstr(V->s,
"nchar=")))
V->topseqlen =
atoi(cp + 6);
if (NULL !=
(cp = strstr(
V->s, "matchchar="))) {
cp += 10;
if (*cp == '\'')
cp++;
else if (*cp == '"')
cp++;
V->matchchar = *cp;
}
}
if (interleaved)
readPAUPinterleaved(V);
else
readPAUPsequential(V);
} break;
/* kPhylip: ! can't determine in middle of file
* which type it is...*/
/* test for interleave or sequential and use
* Phylip4(ileave) or Phylip2 */
case kPhylip2:
readPhylipSequential(V);
break;
case kPhylip4: /* == kPhylip3 */
readPhylipInterleaved(V);
break;
default:
V->err = eUnknownFormat;
break;
case kFitch:
strcpy(V->seqid, V->s);
cgetline(V);
readFitch(V);
break;
case kGCG:
do {
gotuw = (strstr(V->s, "..") !=
NULL);
if (gotuw) readUWGCG(V);
cgetline(V);
} while (!(feof(V->f) || V->allDone));
break;
}
}
V->filestart = false;
V->seq[V->seqlen] = 0; /* stick a string terminator on it */
}
char *readSeqFp(const short whichEntry_, /* index to sequence in file */
FILE *fp_, /* pointer to open seq file */
const long skiplines_,
const short format_, /* sequence file format */
long *seqlen_, /* return seq size */
short *nseq_, /* number of seqs in file, for listSeqs() */
short *error_, /* return error */
char *seqid_) /* return seq name/info */
{
struct ReadSeqVars V;
if (format_ < kMinFormat || format_ > kMaxFormat) {
*error_ = eUnknownFormat;
*seqlen_ = 0;
return NULL;
}
V.choice = whichEntry_;
V.fname = NULL; /* don't know */
V.seq = (char *)calloc(1, kStartLength + 1);
V.maxseq = kStartLength;
V.seqlen = 0;
V.seqid = seqid_;
V.f = fp_;
V.filestart = (ftell(fp_) == 0);
/* !! in sequential read, must remove current seq position from
* choice/whichEntry_ counter !! ... */
if (V.filestart)
V.nseq = 0;
else
V.nseq = *nseq_; /* track where we are in file...*/
*V.seqid = '\0';
V.err = 0;
V.nseq = 0;
V.isseqchar = isSeqChar;
if (V.choice == kListSequences)
; /* leave as is */
else if (V.choice <= 0)
V.choice = 1; /* default ?? */
V.addit = (V.choice > 0);
V.allDone = false;
readSeqMain(&V, skiplines_, format_);
*error_ = V.err;
*seqlen_ = V.seqlen;
*nseq_ = V.nseq;
return V.seq;
}
char *readSeq(const short whichEntry_, /* index to sequence in file */
const char *filename_, /* file name */
const long skiplines_,
const short format_, /* sequence file format */
long *seqlen_, /* return seq size */
short *nseq_, /* number of seqs in file, for listSeqs() */
short *error_, /* return error */
char *seqid_) /* return seq name/info */
{
struct ReadSeqVars V;
if (format_ < kMinFormat || format_ > kMaxFormat) {
*error_ = eUnknownFormat;
*seqlen_ = 0;
return NULL;
}
V.choice = whichEntry_;
V.fname = filename_; /* don't need to copy string, just ptr to it */
V.seq = (char *)calloc(1, kStartLength + 1);
V.maxseq = kStartLength;
V.seqlen = 0;
V.seqid = seqid_;
V.f = NULL;
*V.seqid = '\0';
V.err = 0;
V.nseq = 0;
V.isseqchar = isSeqChar;
if (V.choice == kListSequences)
; /* leave as is */
else if (V.choice <= 0)
V.choice = 1; /* default ?? */
V.addit = (V.choice > 0);
V.allDone = false;
V.f = fopen(V.fname, "r");
V.filestart = true;
readSeqMain(&V, skiplines_, format_);
if (V.f != NULL) fclose(V.f);
*error_ = V.err;
*seqlen_ = V.seqlen;
*nseq_ = V.nseq;
return V.seq;
}
char *listSeqs(const char *filename_, /* file name */
const long skiplines_,
const short format_, /* sequence file format */
short *nseq_, /* number of seqs in file, for listSeqs() */
short *error_) /* return error */
{
char seqid[256];
long seqlen;
return readSeq(kListSequences, filename_, skiplines_, format_, &seqlen,
nseq_, error_, seqid);
}
short seqFileFormat(/* return sequence format number, see ureadseq.h */
const char *filename,
long *skiplines, /* return #lines to skip any junk like mail
header */
short *error) /* return any error value or 0 */
{
FILE *fseq;
short format;
fseq = fopen(filename, "r");
format = seqFileFormatFp(fseq, skiplines, error);
if (fseq != NULL) fclose(fseq);
return format;
}
short seqFileFormatFp(
FILE *fseq,
long *skiplines, /* return #lines to skip any junk like mail header */
short *error) /* return any error value or 0 */
{
boolean foundDNA = false, foundIG = false, foundStrider = false,
foundGB = false, foundPIR = false, foundEMBL = false,
foundNBRF = false, foundPearson = false, foundFitch = false,
foundPhylip = false, foundZuker = false, gotolsen = false,
gotpaup = false, gotasn1 = false, gotuw = false, gotMSF = false,
isfitch = false, isphylip = false, done = false;
short format = kUnknown;
int nlines = 0, k, splen = 0, otherlines = 0, aminolines = 0,
dnalines = 0;
char sp[256];
long linestart = 0;
int maxlines2check = 500;
#define ReadOneLine(sp) \
{ \
done |= (feof(fseq)); \
readline(fseq, sp, &linestart); \
if (!done) { \
splen = strlen(sp); \
++nlines; \
} \
}
*skiplines = 0;
*error = 0;
if (fseq == NULL) {
*error = eFileNotFound;
return kNoformat;
}
while (!done) {
ReadOneLine(sp);
/* check for mailer head & skip past if found */
if (nlines < 4 && !done) {
if ((strstr(sp, "From ") == sp) ||
(strstr(sp, "Received:") == sp)) {
do {
/* skip all lines until find one blank
* line */
ReadOneLine(sp);
if (!done)
for (k = 0; (k < splen) &&
(sp[k] == ' ');
k++)
;
} while ((!done) && (k < splen));
*skiplines = nlines; /* !? do we want #lines or
#bytes ?? */
}
}
if (sp == NULL || *sp == 0)
; /* nada */
/* high probability identities: */
else if (strstr(sp, "MSF:") && strstr(sp, "Type:") &&
strstr(sp, "Check:"))
gotMSF = true;
else if ((strstr(sp, "..") != NULL) &&
(strstr(sp, "Check:") != NULL))
gotuw = true;
else if (strstr(sp, "identity: Data:") != NULL)
gotolsen = true;
else if (strstr(sp, "::=") &&
(strstr(sp, "Bioseq") || /* Bioseq or Bioseq-set */
strstr(sp, "Seq-entry") ||
strstr(
sp,
"Seq-submit"))) /* can we read submit format? */
gotasn1 = true;
else if (strstr(sp, "#NEXUS") == sp)
gotpaup = true;
/* uncertain identities: */
else if (*sp == ';') {
if (strstr(sp, "Strider") != NULL)
foundStrider = true;
else
foundIG = true;
}
else if (strstr(sp, "LOCUS") == sp)
foundGB = true;
else if (strstr(sp, "ORIGIN") == sp)
foundGB = true;
else if (strstr(sp, "ENTRY ") ==
sp) /* ? also (strcmp(sp,"\\\\\\")==0) */
foundPIR = true;
else if (strstr(sp, "SEQUENCE") == sp)
foundPIR = true;
else if (*sp == '>') {
if (sp[3] == ';')
foundNBRF = true;
else
foundPearson = true;
}
else if (strstr(sp, "ID ") == sp)
foundEMBL = true;
else if (strstr(sp, "SQ ") == sp)
foundEMBL = true;
else if (*sp == '(')
foundZuker = true;
else {
if (nlines - *skiplines == 1) {
int ispp = 0, ilen = 0;
sscanf(sp, "%d%d", &ispp, &ilen);
if (ispp > 0 && ilen > 0) isphylip = true;
}
else if (isphylip && nlines - *skiplines == 2) {
int tseq;
tseq = getseqtype(sp + 10, strlen(sp + 10));
if (isalpha(*sp) /* 1st letter in 2nd line must
be of a name */
&& (tseq != kOtherSeq)) /* sequence section
must be okay */
foundPhylip = true;
}
for (k = 0, isfitch = true; isfitch & (k < splen);
k++) {
if (k % 4 == 0)
isfitch &= (sp[k] == ' ');
else
isfitch &= (sp[k] != ' ');
}
if (isfitch & (splen > 20)) foundFitch = true;
/* kRNA && kDNA are fairly certain...*/
switch (getseqtype(sp, splen)) {
case kOtherSeq:
otherlines++;
break;
case kAmino:
if (splen > 20) aminolines++;
break;
case kDNA:
case kRNA:
if (splen > 20) dnalines++;
break;
case kNucleic:
break; /* not much info ? */
}
}
/* pretty certain */
if (gotolsen) {
format = kOlsen;
done = true;
}
else if (gotMSF) {
format = kMSF;
done = true;
}
else if (gotasn1) {
/* !! we need to look further and return kASNseqentry |
* kASNseqset */
/*
seqentry key is Seq-entry ::=
seqset key is Bioseq-set ::=
?? can't read these yet w/ ncbi tools ??
Seq-submit ::=
Bioseq ::= << fails both bioseq-seq and seq-entry
parsers !
*/
if (strstr(sp, "Bioseq-set"))
format = kASNseqset;
else if (strstr(sp, "Seq-entry"))
format = kASNseqentry;
else
format = kASN1; /* other form, we can't yet
read... */
done = true;
}
else if (gotpaup) {
format = kPAUP;
done = true;
}
else if (gotuw) {
if (foundIG)
format =
kIG; /* a TOIG file from GCG for certain */
else
format = kGCG;
done = true;
}
else if ((dnalines > 1) || done || (nlines > maxlines2check)) {
/* decide on most likely format */
/* multichar idents: */
if (foundStrider)
format = kStrider;
else if (foundGB)
format = kGenBank;
else if (foundPIR)
format = kPIR;
else if (foundEMBL)
format = kEMBL;
else if (foundNBRF)
format = kNBRF;
/* single char idents: */
else if (foundIG)
format = kIG;
else if (foundPearson)
format = kPearson;
else if (foundZuker)
format = kZuker;
/* digit ident: */
else if (foundPhylip)
format = kPhylip;
/* spacing ident: */
else if (foundFitch)
format = kFitch;
/* no format chars: */
else if (otherlines > 0)
format = kUnknown;
else if (dnalines > 1)
format = kPlain;
else if (aminolines > 1)
format = kPlain;
else
format = kUnknown;
done = true;
}
/* need this for possible long header in olsen format */
else if (strstr(sp, "): ") != NULL)
maxlines2check++;
}
if (format == kPhylip) {
/* check for interleaved or sequential -- really messy */
int tname, tseq;
long i, j, nspp = 0, nlen = 0, ilen, leaf = 0, seq = 0;
char *ps;
rewind(fseq);
for (i = 0; i < *skiplines; i++) ReadOneLine(sp);
nlines = 0;
ReadOneLine(sp);
sscanf(sp, "%d%d", &nspp, &nlen);
ReadOneLine(sp); /* 1st seq line */
for (ps = sp + 10, ilen = 0; *ps != 0; ps++)
if (isprint(*ps)) ilen++;
for (i = 1; i < nspp; i++) {
ReadOneLine(sp);
tseq = getseqtype(sp + 10, strlen(sp + 10));
tname = getseqtype(sp, 10);
for (j = 0, ps = sp; isspace(*ps) && j < 10; ps++, j++)
;
for (ps = sp; *ps != 0; ps++)
if (isprint(*ps)) ilen++;
/* find probable interleaf or sequential ... */
if (j >= 9)
seq += 10; /* pretty certain not ileaf */
else {
if (tseq != tname)
leaf++;
else
seq++;
if (tname == kDNA || tname == kRNA)
seq++;
else
leaf++;
}
if (ilen <= nlen && j < 9) {
if (tname == kOtherSeq)
leaf += 10;
else if (tname == kAmino || tname == kDNA ||
tname == kRNA)
seq++;
else
leaf++;
}
else if (ilen > nlen) {
ilen = 0;
}
}
for (nspp *= 2; i < nspp;
i++) { /* this should be only bases if interleaf */
ReadOneLine(sp);
tseq = getseqtype(sp + 10, strlen(sp + 10));
tname = getseqtype(sp, 10);
for (ps = sp; *ps != 0; ps++)
if (isprint(*ps)) ilen++;
for (j = 0, ps = sp; isspace(*ps) && j < 10; ps++, j++)
;
if (j < 9) {
if (tname == kOtherSeq) seq += 10;
if (tseq != tname)
seq++;
else
leaf++;
if (tname == kDNA || tname == kRNA)
leaf++;
else
seq++;
}
if (ilen > nlen) {
if (j > 9)
leaf += 10; /* must be a name here for
sequent */
else if (tname == kOtherSeq)
seq += 10;
ilen = 0;
}
}
if (leaf > seq)
format = kPhylip4;
else
format = kPhylip2;
}
return (format);
#undef ReadOneLine
} /* SeqFileFormat */
unsigned long GCGchecksum(const char *seq, const long seqlen,
unsigned long *checktotal)
/* GCGchecksum */
{
register long i, check = 0, count = 0;
for (i = 0; i < seqlen; i++) {
count++;
check += count * to_upper(seq[i]);
if (count == 57) count = 0;
}
check %= 10000;
*checktotal += check;
*checktotal %= 10000;
return check;
}
/* Table of CRC-32's of all single byte values (made by makecrc.c of ZIP source)
*/
const unsigned long crctab[] = {
0x00000000L, 0x77073096L, 0xee0e612cL, 0x990951baL, 0x076dc419L,
0x706af48fL, 0xe963a535L, 0x9e6495a3L, 0x0edb8832L, 0x79dcb8a4L,
0xe0d5e91eL, 0x97d2d988L, 0x09b64c2bL, 0x7eb17cbdL, 0xe7b82d07L,
0x90bf1d91L, 0x1db71064L, 0x6ab020f2L, 0xf3b97148L, 0x84be41deL,
0x1adad47dL, 0x6ddde4ebL, 0xf4d4b551L, 0x83d385c7L, 0x136c9856L,
0x646ba8c0L, 0xfd62f97aL, 0x8a65c9ecL, 0x14015c4fL, 0x63066cd9L,
0xfa0f3d63L, 0x8d080df5L, 0x3b6e20c8L, 0x4c69105eL, 0xd56041e4L,
0xa2677172L, 0x3c03e4d1L, 0x4b04d447L, 0xd20d85fdL, 0xa50ab56bL,
0x35b5a8faL, 0x42b2986cL, 0xdbbbc9d6L, 0xacbcf940L, 0x32d86ce3L,
0x45df5c75L, 0xdcd60dcfL, 0xabd13d59L, 0x26d930acL, 0x51de003aL,
0xc8d75180L, 0xbfd06116L, 0x21b4f4b5L, 0x56b3c423L, 0xcfba9599L,
0xb8bda50fL, 0x2802b89eL, 0x5f058808L, 0xc60cd9b2L, 0xb10be924L,
0x2f6f7c87L, 0x58684c11L, 0xc1611dabL, 0xb6662d3dL, 0x76dc4190L,
0x01db7106L, 0x98d220bcL, 0xefd5102aL, 0x71b18589L, 0x06b6b51fL,
0x9fbfe4a5L, 0xe8b8d433L, 0x7807c9a2L, 0x0f00f934L, 0x9609a88eL,
0xe10e9818L, 0x7f6a0dbbL, 0x086d3d2dL, 0x91646c97L, 0xe6635c01L,
0x6b6b51f4L, 0x1c6c6162L, 0x856530d8L, 0xf262004eL, 0x6c0695edL,
0x1b01a57bL, 0x8208f4c1L, 0xf50fc457L, 0x65b0d9c6L, 0x12b7e950L,
0x8bbeb8eaL, 0xfcb9887cL, 0x62dd1ddfL, 0x15da2d49L, 0x8cd37cf3L,
0xfbd44c65L, 0x4db26158L, 0x3ab551ceL, 0xa3bc0074L, 0xd4bb30e2L,
0x4adfa541L, 0x3dd895d7L, 0xa4d1c46dL, 0xd3d6f4fbL, 0x4369e96aL,
0x346ed9fcL, 0xad678846L, 0xda60b8d0L, 0x44042d73L, 0x33031de5L,
0xaa0a4c5fL, 0xdd0d7cc9L, 0x5005713cL, 0x270241aaL, 0xbe0b1010L,
0xc90c2086L, 0x5768b525L, 0x206f85b3L, 0xb966d409L, 0xce61e49fL,
0x5edef90eL, 0x29d9c998L, 0xb0d09822L, 0xc7d7a8b4L, 0x59b33d17L,
0x2eb40d81L, 0xb7bd5c3bL, 0xc0ba6cadL, 0xedb88320L, 0x9abfb3b6L,
0x03b6e20cL, 0x74b1d29aL, 0xead54739L, 0x9dd277afL, 0x04db2615L,
0x73dc1683L, 0xe3630b12L, 0x94643b84L, 0x0d6d6a3eL, 0x7a6a5aa8L,
0xe40ecf0bL, 0x9309ff9dL, 0x0a00ae27L, 0x7d079eb1L, 0xf00f9344L,
0x8708a3d2L, 0x1e01f268L, 0x6906c2feL, 0xf762575dL, 0x806567cbL,
0x196c3671L, 0x6e6b06e7L, 0xfed41b76L, 0x89d32be0L, 0x10da7a5aL,
0x67dd4accL, 0xf9b9df6fL, 0x8ebeeff9L, 0x17b7be43L, 0x60b08ed5L,
0xd6d6a3e8L, 0xa1d1937eL, 0x38d8c2c4L, 0x4fdff252L, 0xd1bb67f1L,
0xa6bc5767L, 0x3fb506ddL, 0x48b2364bL, 0xd80d2bdaL, 0xaf0a1b4cL,
0x36034af6L, 0x41047a60L, 0xdf60efc3L, 0xa867df55L, 0x316e8eefL,
0x4669be79L, 0xcb61b38cL, 0xbc66831aL, 0x256fd2a0L, 0x5268e236L,
0xcc0c7795L, 0xbb0b4703L, 0x220216b9L, 0x5505262fL, 0xc5ba3bbeL,
0xb2bd0b28L, 0x2bb45a92L, 0x5cb36a04L, 0xc2d7ffa7L, 0xb5d0cf31L,
0x2cd99e8bL, 0x5bdeae1dL, 0x9b64c2b0L, 0xec63f226L, 0x756aa39cL,
0x026d930aL, 0x9c0906a9L, 0xeb0e363fL, 0x72076785L, 0x05005713L,
0x95bf4a82L, 0xe2b87a14L, 0x7bb12baeL, 0x0cb61b38L, 0x92d28e9bL,
0xe5d5be0dL, 0x7cdcefb7L, 0x0bdbdf21L, 0x86d3d2d4L, 0xf1d4e242L,
0x68ddb3f8L, 0x1fda836eL, 0x81be16cdL, 0xf6b9265bL, 0x6fb077e1L,
0x18b74777L, 0x88085ae6L, 0xff0f6a70L, 0x66063bcaL, 0x11010b5cL,
0x8f659effL, 0xf862ae69L, 0x616bffd3L, 0x166ccf45L, 0xa00ae278L,
0xd70dd2eeL, 0x4e048354L, 0x3903b3c2L, 0xa7672661L, 0xd06016f7L,
0x4969474dL, 0x3e6e77dbL, 0xaed16a4aL, 0xd9d65adcL, 0x40df0b66L,
0x37d83bf0L, 0xa9bcae53L, 0xdebb9ec5L, 0x47b2cf7fL, 0x30b5ffe9L,
0xbdbdf21cL, 0xcabac28aL, 0x53b39330L, 0x24b4a3a6L, 0xbad03605L,
0xcdd70693L, 0x54de5729L, 0x23d967bfL, 0xb3667a2eL, 0xc4614ab8L,
0x5d681b02L, 0x2a6f2b94L, 0xb40bbe37L, 0xc30c8ea1L, 0x5a05df1bL,
0x2d02ef8dL};
unsigned long CRC32checksum(const char *seq, const long seqlen,
unsigned long *checktotal)
/*CRC32checksum: modified from CRC-32 algorithm found in ZIP compression source
*/
{
register unsigned long c = 0xffffffffL;
register long n = seqlen;
while (n--) {
c = crctab[((int)c ^ (to_upper(*seq))) & 0xff] ^ (c >> 8);
seq++; /* fixed aug'98 finally */
}
c = c ^ 0xffffffffL;
*checktotal += c;
return c;
}
short getseqtype(const char *seq, const long seqlen)
{ /* return sequence kind: kDNA, kRNA, kProtein, kOtherSeq, ??? */
char c;
short i, maxtest;
short na = 0, aa = 0, po = 0, nt = 0, nu = 0, ns = 0, no = 0;
maxtest = min(300, seqlen);
for (i = 0; i < maxtest; i++) {
c = to_upper(seq[i]);
if (strchr(protonly, c))
po++;
else if (strchr(primenuc, c)) {
na++;
if (c == 'T')
nt++;
else if (c == 'U')
nu++;
}
else if (strchr(aminos, c))
aa++;
else if (strchr(seqsymbols, c))
ns++;
else if (isalpha(c))
no++;
}
if ((no > 0) || (po + aa + na == 0)) return kOtherSeq;
/* ?? test for probability of kOtherSeq ?, e.g.,
else if (po+aa+na / maxtest < 0.70) return kOtherSeq;
*/
else if (po > 0)
return kAmino;
else if (aa == 0) {
if (nu > nt)
return kRNA;
else
return kDNA;
}
else if (na > aa)
return kNucleic;
else
return kAmino;
} /* getseqtype */
char *compressSeq(const char gapc, const char *seq, const long seqlen,
long *newlen)
{
register char *a, *b;
register long i;
char *newseq;
*newlen = 0;
if (!seq) return NULL;
newseq = (char *)malloc(seqlen + 1);
if (!newseq) return NULL;
for (a = (char *)seq, b = newseq, i = 0; *a != 0; a++)
if (*a != gapc) {
*b++ = *a;
i++;
}
*b = '\0';
newseq = (char *)realloc(newseq, i + 1);
*newlen = i;
return newseq;
}
/***
char *rtfhead = "{\\rtf1\\defformat\\mac\\deff2 \
{\\fonttbl\
{\\f1\\fmodern Courier;}{\\f2\\fmodern Monaco;}\
{\\f3\\fswiss Helvetica;}{\\f4\\fswiss Geneva;}\
{\\f5\\froman Times;}{\\f6\\froman Palatino;}\
{\\f7\\froman New Century Schlbk;}{\\f8\\ftech Symbol;}}\
{\\stylesheet\
{\\s1 \\f5\\fs20 \\sbasedon0\\snext1 name;}\
{\\s2 \\f3\\fs20 \\sbasedon0\\snext2 num;}\
{\\s3 \\f1\\f21 \\sbasedon0\\snext3 seq;}}";
char *rtftail = "}";
****/
short writeSeq(FILE *outf, const char *seq, const long seqlen,
const short outform, const char *seqid)
/* dump sequence to standard output */
{
const short kSpaceAll = -9;
#define kMaxseqwidth 250
boolean baseonlynum =
false; /* nocountsymbols -- only count true bases, not "-" */
short numline = 0; /* only true if we are writing seq number line (for
interleave) */
boolean numright = false, numleft = false;
boolean nameright = false, nameleft = false;
short namewidth = 8, numwidth = 8;
short spacer = 0, width = 50, tab = 0;
/* new parameters: width, spacer, those above... */
short linesout = 0, seqtype = kNucleic;
long i, j, l, l1, ibase;
char idword[31], endstr[10];
char seqnamestore[128], *seqname = seqnamestore;
char s[kMaxseqwidth], *cp;
char nameform[10], numform[10], nocountsymbols[10];
unsigned long checksum = 0, checktotal = 0;
gPretty.atseq++;
skipwhitespace(seqid);
l = min(128, strlen(seqid));
strncpy(seqnamestore, seqid, l);
seqname[l] = 0;
sscanf(seqname, "%30s", idword);
sprintf(numform, "%d", seqlen);
numwidth = strlen(numform) + 1;
nameform[0] = '\0';
if (strstr(seqname, "checksum") != NULL) {
cp = strstr(seqname, "bases");
if (cp != NULL) {
for (; (cp != seqname) && (*cp != ','); cp--)
;
if (cp != seqname) *cp = 0;
}
}
strcpy(endstr, "");
l1 = 0;
if (outform == kGCG || outform == kMSF)
checksum = GCGchecksum(seq, seqlen, &checktotal);
else
checksum = seqchecksum(seq, seqlen, &checktotal);
switch (outform) {
case kPlain:
case kUnknown: /* no header, just sequence */
strcpy(endstr, "\n"); /* end w/ extra blank line */
break;
case kOlsen: /* Olsen seq. editor takes plain nucs OR Genbank */
case kGenBank:
fprintf(outf, "LOCUS %s %d bp\n", idword,
seqlen);
fprintf(outf,
"DEFINITION %s, %d bases, %X checksum.\n",
seqname, seqlen, checksum);
/* fprintf(outf,"ACCESSION %s\n", accnum); */
fprintf(outf, "ORIGIN \n");
spacer = 11;
numleft = true;
numwidth = 8; /* dgg. 1Feb93, patch for GDE fail to read
short numwidth */
strcpy(endstr, "\n//");
linesout += 4;
break;
case kPIR:
/* somewhat like genbank... \\\*/
/* fprintf(outf,"\\\\\\\n"); << only at top of file, not
* each entry... */
fprintf(outf, "ENTRY %s \n", idword);
fprintf(outf,
"TITLE %s, %d bases, %X checksum.\n",
seqname, seqlen, checksum);
/* fprintf(outf,"ACCESSION %s\n", accnum); */
fprintf(outf, "SEQUENCE \n");
numwidth = 7;
width = 30;
spacer = kSpaceAll;
numleft = true;
strcpy(endstr, "\n///");
/* run a top number line for PIR */
for (j = 0; j < numwidth; j++) fputc(' ', outf);
for (j = 5; j <= width; j += 5)
fprintf(outf, "%10d", j);
fputc('\n', outf);
linesout += 5;
break;
case kNBRF:
if (getseqtype(seq, seqlen) == kAmino)
fprintf(outf, ">P1;%s\n", idword);
else
fprintf(outf, ">DL;%s\n", idword);
fprintf(outf, "%s, %d bases, %X checksum.\n", seqname,
seqlen, checksum);
spacer = 11;
strcpy(endstr, "*\n");
linesout += 3;
break;
case kEMBL:
fprintf(outf, "ID %s\n", idword);
/* fprintf(outf,"AC %s\n", accnum); */
fprintf(outf, "DE %s, %d bases, %X checksum.\n",
seqname, seqlen, checksum);
fprintf(outf, "SQ %d BP\n", seqlen);
strcpy(endstr, "\n//"); /* 11Oct90: bug fix*/
tab = 4; /** added 31jan91 */
spacer = 11; /** added 31jan91 */
width = 60;
linesout += 4;
break;
case kGCG:
fprintf(outf, "%s\n", seqname);
/* fprintf(outf,"ACCESSION %s\n", accnum); */
fprintf(outf,
" %s Length: %d (today) Check: %d ..\n",
idword, seqlen, checksum);
spacer = 11;
numleft = true;
strcpy(endstr, "\n"); /* this is insurance to help
prevent misreads at eof */
linesout += 3;
break;
case kStrider: /* ?? map ?*/
fprintf(outf, "; ### from DNA Strider ;-)\n");
fprintf(
outf,
"; DNA sequence %s, %d bases, %X checksum.\n;\n",
seqname, seqlen, checksum);
strcpy(endstr, "\n//");
linesout += 3;
break;
case kFitch:
fprintf(outf, "%s, %d bases, %X checksum.\n", seqname,
seqlen, checksum);
spacer = 4;
width = 60;
linesout += 1;
break;
case kPhylip2:
case kPhylip4:
/* this is version 3.2/3.4 -- simplest way to write
version 3.3 is to write as version 3.2, then
re-read file and interleave the species lines */
if (strlen(idword) > 10) idword[10] = 0;
fprintf(outf, "%-10s ", idword);
l1 = -1;
tab = 12;
spacer = 11;
break;
case kASN1:
seqtype = getseqtype(seq, seqlen);
switch (seqtype) {
case kDNA:
cp = "dna";
break;
case kRNA:
cp = "rna";
break;
case kNucleic:
cp = "na";
break;
case kAmino:
cp = "aa";
break;
case kOtherSeq:
cp = "not-set";
break;
}
fprintf(outf, " seq {\n");
fprintf(outf, " id { local id %d },\n",
gPretty.atseq);
fprintf(outf, " descr { title \"%s\" },\n", seqid);
fprintf(outf, " inst {\n");
fprintf(outf,
" repr raw, mol %s, length %d, topology "
"linear,\n",
cp, seqlen);
fprintf(outf, " seq-data\n");
if (seqtype == kAmino)
fprintf(outf, " iupacaa \"");
else
fprintf(outf, " iupacna \"");
l1 = 17;
spacer = 0;
width = 78;
tab = 0;
strcpy(endstr, "\"\n } } ,");
linesout += 7;
break;
case kPAUP:
nameleft = true;
namewidth = 9;
spacer = 21;
width = 100;
tab = 0; /* 1; */
/* strcpy(endstr,";\nend;"); << this is end of all
* seqs.. */
/* do a header comment line for paup */
fprintf(outf, "[Name: %-16s Len:%6d Check: %8X]\n",
idword, seqlen, checksum);
linesout += 1;
break;
case kPretty:
numline = gPretty.numline;
baseonlynum = gPretty.baseonlynum;
namewidth = gPretty.namewidth;
numright = gPretty.numright;
numleft = gPretty.numleft;
nameright = gPretty.nameright;
nameleft = gPretty.nameleft;
spacer = gPretty.spacer + 1;
width = gPretty.seqwidth;
tab = gPretty.tab;
/* also add rtf formatting w/ font, size, style */
if (gPretty.nametop) {
fprintf(outf,
"Name: %-16s Len:%6d Check: %8X\n",
idword, seqlen, checksum);
linesout++;
}
break;
case kMSF:
fprintf(
outf,
" Name: %-16s Len:%6d Check: %5d Weight: 1.00\n",
idword, seqlen, checksum);
linesout++;
nameleft = true;
namewidth = 15; /* need MAX namewidth here... */
sprintf(nameform, "%%+%ds ", namewidth);
spacer = 11;
width = 50;
tab = 0; /* 1; */
break;
case kIG:
fprintf(outf, ";%s, %d bases, %X checksum.\n", seqname,
seqlen, checksum);
fprintf(outf, "%s\n", idword);
strcpy(endstr, "1"); /* == linear dna */
linesout += 2;
break;
default:
case kZuker: /* don't attempt Zuker's ftn format */
case kPearson:
fprintf(outf, ">%s, %d bases, %X checksum.\n", seqname,
seqlen, checksum);
linesout += 1;
break;
}
if (*nameform == 0)
sprintf(nameform, "%%%d.%ds ", namewidth, namewidth);
if (numline)
sprintf(numform, "%%%ds ", numwidth);
else
sprintf(numform, "%%%dd ", numwidth);
strcpy(nocountsymbols, kNocountsymbols);
if (baseonlynum) {
if (strchr(nocountsymbols, gPretty.gapchar) == NULL) {
strcat(nocountsymbols, " ");
nocountsymbols[strlen(nocountsymbols) - 1] =
gPretty.gapchar;
}
if (gPretty.domatch &&
(cp = strchr(nocountsymbols, gPretty.matchchar)) != NULL) {
*cp = ' ';
}
}
if (numline) {
*idword = 0;
}
width = min(width, kMaxseqwidth);
for (i = 0, l = 0, ibase = 1; i < seqlen;) {
if (l1 < 0)
l1 = 0;
else if (l1 == 0) {
if (nameleft) fprintf(outf, nameform, idword);
if (numleft) {
if (numline)
fprintf(outf, numform, "");
else
fprintf(outf, numform, ibase);
}
for (j = 0; j < tab; j++) fputc(' ', outf);
}
l1++; /* don't count spaces for width*/
if (numline) {
if (spacer == kSpaceAll ||
(spacer != 0 && (l + 1) % spacer == 1)) {
if (numline == 1) fputc(' ', outf);
s[l++] = ' ';
}
if (l1 % 10 == 1 || l1 == width) {
if (numline == 1) fprintf(outf, "%-9d ", i + 1);
s[l++] = '|'; /* == put a number here */
}
else
s[l++] = ' ';
i++;
}
else {
if (spacer == kSpaceAll ||
(spacer != 0 && (l + 1) % spacer == 1))
s[l++] = ' ';
if (!baseonlynum)
ibase++;
else if (0 == strchr(nocountsymbols, seq[i]))
ibase++;
s[l++] = seq[i++];
}
if (l1 == width || i == seqlen) {
if (outform == kPretty)
for (; l1 < width; l1++) {
if (spacer == kSpaceAll ||
(spacer != 0 &&
(l + 1) % spacer == 1))
s[l++] = ' ';
s[l++] = ' '; /* pad w/ blanks */
}
s[l] = '\0';
l = 0;
l1 = 0;
if (numline) {
if (numline == 2)
fprintf(
outf, "%s",
s); /* finish numberline ! and | */
}
else {
if (i == seqlen)
fprintf(outf, "%s%s", s, endstr);
else
fprintf(outf, "%s", s);
if (numright || nameright) fputc(' ', outf);
if (numright) fprintf(outf, numform, ibase - 1);
if (nameright) fprintf(outf, nameform, idword);
}
fputc('\n', outf);
linesout++;
}
}
return linesout;
} /*writeSeq*/
/* End file: ureadseq.c */
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