Date: Tue, 21 Aug 2001 20:24:27 +1000 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/29922: New port: biology/seqio - a set of C functions to read/write bilogical sequences Message-ID: <200108211024.f7LAORb59595@dt.home>
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>Number: 29922
>Category: ports
>Synopsis: New port: biology/seqio - a set of C functions to read/write bilogical sequences
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Tue Aug 21 03:30:06 PDT 2001
>Closed-Date:
>Last-Modified:
>Originator: Tony Maher
>Release: FreeBSD 4.4-RC i386
>Organization:
Biolateral
>Environment:
System: FreeBSD dt.home 4.4-RC FreeBSD 4.4-RC #6: Fri Aug 17 14:21:47 EST 2001 root@dt.home:/usr/src/sys/compile/DT i386
>Description:
"The SEQIO package is a set of C functions which can read and write
biological sequence files formatted using various file formats and
which can be used to perform database searches on biological databases."
- from the README file
It also has 4 useful executables that utilize seqio.
>How-To-Repeat:
>Fix:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# seqio
# seqio/files
# seqio/files/patch-grepseq
# seqio/files/patch-fmtseq
# seqio/files/patch-seqio
# seqio/files/patch-Makefile
# seqio/pkg-plist
# seqio/pkg-descr
# seqio/pkg-comment
# seqio/distinfo
# seqio/Makefile
#
echo c - seqio
mkdir -p seqio > /dev/null 2>&1
echo c - seqio/files
mkdir -p seqio/files > /dev/null 2>&1
echo x - seqio/files/patch-grepseq
sed 's/^X//' >seqio/files/patch-grepseq << 'END-of-seqio/files/patch-grepseq'
X--- grepseq.c.orig Sat Aug 18 16:19:15 2001
X+++ grepseq.c Sat Aug 18 16:37:58 2001
X@@ -18,7 +18,6 @@
X #include <string.h>
X #include "seqio.h"
X
X-extern char *sys_errlist[];
X
X #define ASCII 4
X
X@@ -475,7 +474,7 @@
X ascii_alpha_mask[num] |= mask;
X }
X else
X- ascii_alpha_mask[*s] |= mask;
X+ ascii_alpha_mask[(int) *s] |= mask;
X break;
X
X case '.':
X@@ -518,7 +517,7 @@
X ascii_alpha_mask[num] |= mask;
X }
X else
X- ascii_alpha_mask[*s] |= mask;
X+ ascii_alpha_mask[(int) *s] |= mask;
X }
X else {
X if (dna_flag) {
X@@ -526,17 +525,17 @@
X dna_flag = 0;
X else
X for ( ; *t; t++)
X- dna_alpha_mask[*t] |= mask;
X+ dna_alpha_mask[(int) *t] |= mask;
X }
X if (prt_flag) {
X if ((t = prt_expand(*s)) == NULL)
X prt_flag = 0;
X else
X for ( ; *t; t++)
X- prt_alpha_mask[*t] |= mask;
X+ prt_alpha_mask[(int) *t] |= mask;
X }
X
X- ascii_alpha_mask[*s] |= mask;
X+ ascii_alpha_mask[(int) *s] |= mask;
X }
X }
X
X@@ -557,17 +556,17 @@
X dna_flag = 0;
X else
X for ( ; *t; t++)
X- dna_alpha_mask[*t] |= mask;
X+ dna_alpha_mask[(int) *t] |= mask;
X }
X if (prt_flag) {
X if ((t = prt_expand(*s)) == NULL)
X prt_flag = 0;
X else
X for ( ; *t; t++)
X- prt_alpha_mask[*t] |= mask;
X+ prt_alpha_mask[(int) *t] |= mask;
X }
X
X- ascii_alpha_mask[*s] |= mask;
X+ ascii_alpha_mask[(int) *s] |= mask;
X }
X
X /*
X@@ -677,16 +676,16 @@
X */
X if (num_errors == 0) {
X score = 0;
X- while ((ch = *s) && table[ch] &&
X- !((masklist0 = ((masklist0 << 1) & alpha_mask[*s]) + 1) &
X+ while ((ch = *s) && table[(int) ch] &&
X+ !((masklist0 = ((masklist0 << 1) & alpha_mask[(int) *s]) + 1) &
X accept_mask))
X s++;
X }
X else if (num_errors == 1) {
X score = -1;
X if (misonly_flag) {
X- while ((ch = *s) && table[ch]) {
X- chmask = alpha_mask[ch];
X+ while ((ch = *s) && table[(int) ch]) {
X+ chmask = alpha_mask[(int) ch];
X last_mask = masklist0;
X masklist0 = ((masklist0 << 1) & chmask) + 1;
X masklist1 = ((masklist1 << 1) & chmask) | (last_mask << 1);
X@@ -703,8 +702,8 @@
X }
X }
X else {
X- while ((ch = *s) && table[ch]) {
X- chmask = alpha_mask[ch];
X+ while ((ch = *s) && table[(int) ch]) {
X+ chmask = alpha_mask[(int) ch];
X last_mask = masklist0;
X masklist0 = ((masklist0 << 1) & chmask) + 1;
X masklist1 = ((masklist1 << 1) & chmask) | /* match */
X@@ -727,8 +726,8 @@
X else if (num_errors == 2) {
X score = -1;
X if (misonly_flag) {
X- while ((ch = *s) && table[ch]) {
X- chmask = alpha_mask[ch];
X+ while ((ch = *s) && table[(int) ch]) {
X+ chmask = alpha_mask[(int) ch];
X last_mask = masklist0;
X masklist0 = ((masklist0 << 1) & chmask) + 1;
X newmask = ((masklist1 << 1) & chmask) | (last_mask << 1);
X@@ -752,8 +751,8 @@
X }
X }
X else {
X- while ((ch = *s) && table[ch]) {
X- chmask = alpha_mask[ch];
X+ while ((ch = *s) && table[(int) ch]) {
X+ chmask = alpha_mask[(int) ch];
X last_mask = masklist0;
X masklist0 = ((masklist0 << 1) & chmask) + 1;
X newmask = ((masklist1 << 1) & chmask) | /* match */
X@@ -785,8 +784,8 @@
X }
X else if (misonly_flag) {
X score = -1;
X- while ((ch = *s) && table[ch]) {
X- chmask = alpha_mask[ch];
X+ while ((ch = *s) && table[(int) ch]) {
X+ chmask = alpha_mask[(int) ch];
X
X last_mask = masklist[0];
X masklist[0] = ((masklist[0] << 1) & chmask) + 1;
X@@ -808,8 +807,8 @@
X }
X else {
X score = -1;
X- while ((ch = *s) && table[ch]) {
X- chmask = alpha_mask[ch];
X+ while ((ch = *s) && table[(int) ch]) {
X+ chmask = alpha_mask[(int) ch];
X
X last_mask = masklist[0];
X masklist[0] = ((masklist[0] << 1) & chmask) + 1;
X@@ -835,7 +834,7 @@
X
X if (!ch)
X break;
X- else if (!table[ch]) {
X+ else if (!table[(int) ch]) {
X fprintf(stderr, "%s, entry %d: Sequence contains invalid characters.\n",
X seqffilename(sfp, 0), seqfentryno(sfp));
X return NULL;
END-of-seqio/files/patch-grepseq
echo x - seqio/files/patch-fmtseq
sed 's/^X//' >seqio/files/patch-fmtseq << 'END-of-seqio/files/patch-fmtseq'
X--- fmtseq.c.orig Wed Jul 10 12:58:39 1996
X+++ fmtseq.c Tue Aug 21 13:17:23 2001
X@@ -37,7 +37,6 @@
X #include <sys/stat.h>
X #include "seqio.h"
X
X-extern char *sys_errlist[];
X
X
X #ifdef WIN32
X@@ -70,6 +69,7 @@
X #define ASK 2
X #define ITEMLIST 3
X
X+#define MAXLINE 128
X
X int pretty_flag, pretty_count;
X FILE *fpout;
X@@ -81,7 +81,7 @@
X } pretty;
X
X
X-char dna_complement[128], rna_complement[128];
X+char dna_complement[MAXLINE], rna_complement[MAXLINE];
X
X
X /*
X@@ -222,7 +222,7 @@
X void print_options(int flag)
X {
X int i, j;
X- char line[128];
X+ char line[MAXLINE];
X
X printf("Program Options (text in [...] is optional):\n");
X printf(" -al[l] select all sequences\n");
X@@ -249,7 +249,7 @@
X
X if (flag) {
X printf("More? ");
X- gets(line);
X+ fgets(line,MAXLINE-1,stdin);
X if (line[0] == 'q' || line[0] == 'Q')
X return;
X }
X@@ -264,7 +264,7 @@
X
X if (flag) {
X printf("More? ");
X- gets(line);
X+ fgets(line,MAXLINE-1,stdin);
X if (line[0] == 'q' || line[0] == 'Q')
X return;
X }
X@@ -1646,7 +1646,7 @@
X s = line;
X while (*s == '\0') {
X printf("Enter: ");
X- gets(line);
X+ fgets(line,MAXLINE-1,stdin);
X for (s=line; *s && isspace(*s); s++) ;
X }
X printf("----------------------\n\n");
X@@ -1701,7 +1701,7 @@
X {
X static char defch = 'y';
X int init_print, count;
X- char *s, *entry, *eptr, line[128];
X+ char *s, *entry, *eptr, line[MAXLINE];
X
X putchar('\n');
X if (seqcount == 1) {
X@@ -1717,7 +1717,7 @@
X eptr = entry = NULL;
X while (1) {
X printf("Select? [%c] ", defch);
X- gets(line);
X+ fgets(line,MAXLINE-1,stdin);
X
X if (line[0] == '\0')
X line[0] = defch;
X@@ -1771,7 +1771,7 @@
X SEQINFO *info, int mode)
X {
X int len;
X- char *temp, tempbuffer[128];
X+ char *temp, tempbuffer[MAXLINE];
X
X if (buf != NULL)
X temp = buf;
X@@ -1803,7 +1803,7 @@
X
X int pretty_store(char *seq, int seqlen, SEQINFO *info)
X {
X- char buffer[128];
X+ char buffer[MAXLINE];
X
X if (pretty_count == psize) {
X if (psize == 0) {
X@@ -2582,7 +2582,7 @@
X
X void blastout_store(SEQFILE *sfp, char *seq, int seqlen, SEQINFO *info)
X {
X- static otherstrand = 0;
X+ static int otherstrand = 0;
X int pos, al_start, ingap, len;
X char *s, *t1, *entry, *end, *line1, *line2;
X ALIGN newalign;
X@@ -3017,7 +3017,7 @@
X {
X int i;
X
X- for (i=0; i < 128; i++)
X+ for (i=0; i < MAXLINE; i++)
X dna_complement[i] = dna_complement[i] = i;
X
X dna_complement['a'] = 't'; dna_complement['A'] = 'T';
END-of-seqio/files/patch-fmtseq
echo x - seqio/files/patch-seqio
sed 's/^X//' >seqio/files/patch-seqio << 'END-of-seqio/files/patch-seqio'
X--- seqio.c.orig Sat Aug 18 16:20:53 2001
X+++ seqio.c Sat Aug 18 16:21:23 2001
X@@ -147,7 +147,6 @@
X * files, and replacement functions for system calls that don't exist on
X * one or more machines.
X */
X-extern char *sys_errlist[];
X
X #if defined(__sun) && !defined(FILENAME_MAX)
X #include <sys/param.h>
X@@ -158,7 +157,6 @@
X static int ctype_initflag = 0;
X static char tubuf[384], *tuary;
X
X-#define toupper(chr) tuary[(int) (chr)]
X
X static void init_ctype(void)
X {
END-of-seqio/files/patch-seqio
echo x - seqio/files/patch-Makefile
sed 's/^X//' >seqio/files/patch-Makefile << 'END-of-seqio/files/patch-Makefile'
X--- Makefile.orig Tue Aug 21 12:50:44 2001
X+++ Makefile Tue Aug 21 12:51:13 2001
X@@ -12,7 +12,7 @@
X CFLAGS= -g -O2 -Wall -Wshadow
X
X
X-all: grepseq fmtseq idxseq typeseq wcseq examples
X+all: grepseq fmtseq idxseq typeseq wcseq
X
X grepseq: grepseq.o seqio.o
X $(CC) $(CFLAGS) -o grepseq grepseq.o seqio.o
END-of-seqio/files/patch-Makefile
echo x - seqio/pkg-plist
sed 's/^X//' >seqio/pkg-plist << 'END-of-seqio/pkg-plist'
Xbin/fmtseq
Xbin/grepseq
Xbin/idxseq
Xbin/typeseq
Xbin/wcseq
Xshare/doc/seqio/html/bigaln_example.html
Xshare/doc/seqio/html/examples_doc.html
Xshare/doc/seqio/html/fmtseq_doc.html
Xshare/doc/seqio/html/idxseq_doc.html
Xshare/doc/seqio/html/seqio.html
Xshare/doc/seqio/html/seqio_bioseq.html
Xshare/doc/seqio/html/seqio_changes.html
Xshare/doc/seqio/html/seqio_doc.html
Xshare/doc/seqio/html/seqio_format.html
Xshare/doc/seqio/html/seqio_progr.html
Xshare/doc/seqio/html/seqio_qref.html
Xshare/doc/seqio/html/seqio_readme.html
Xshare/doc/seqio/html/seqio_toc.html
Xshare/doc/seqio/html/seqio_todo.html
Xshare/doc/seqio/html/seqio_user.html
Xshare/doc/seqio/bioseq.txt
Xshare/doc/seqio/examples.doc
Xshare/doc/seqio/fmtseq.doc
Xshare/doc/seqio/format.doc
Xshare/doc/seqio/idxseq.doc
Xshare/doc/seqio/programr.doc
Xshare/doc/seqio/quickref.doc
Xshare/doc/seqio/seqio.doc
Xshare/doc/seqio/user.doc
Xshare/examples/seqio/example1.c
Xshare/examples/seqio/example2.c
Xshare/examples/seqio/example3.c
Xshare/examples/seqio/example4.c
Xshare/examples/seqio/seqio.c
Xshare/examples/seqio/seqio.h
Xshare/examples/seqio/Makefile
X@dirrm share/doc/seqio/html
X@dirrm share/doc/seqio
X@dirrm share/examples/seqio
END-of-seqio/pkg-plist
echo x - seqio/pkg-descr
sed 's/^X//' >seqio/pkg-descr << 'END-of-seqio/pkg-descr'
X"The SEQIO package is a set of C functions which can read and write
Xbiological sequence files formatted using various file formats and which
Xcan be used to perform database searches on biological databases."
X- from the README file
X
XWWW: http://www.cs.ucdavis.edu/~gusfield/seqio.html
X
X--
XTony Maher <tonym@biolateral.com.au>
END-of-seqio/pkg-descr
echo x - seqio/pkg-comment
sed 's/^X//' >seqio/pkg-comment << 'END-of-seqio/pkg-comment'
XA set of C functions which can read/write biological sequence files
END-of-seqio/pkg-comment
echo x - seqio/distinfo
sed 's/^X//' >seqio/distinfo << 'END-of-seqio/distinfo'
XMD5 (seqio.tar.gz) = c8e5d44485c8202082d4cfa516f9e0db
END-of-seqio/distinfo
echo x - seqio/Makefile
sed 's/^X//' >seqio/Makefile << 'END-of-seqio/Makefile'
X# New ports collection makefile for: seqio
X# Date created: 17 August 2001
X# Whom: Tony Maher
X#
X# $FreeBSD$
X#
X
XPORTNAME= seqio
XPORTVERSION= 1.2.2
XCATEGORIES= biology
XMASTER_SITES= http://www.cs.ucdavis.edu/~gusfield/
XDISTNAME= ${PORTNAME}
X
XMAINTAINER= tonym@biolateral.com.au
X
XWRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
X
XEXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME}
XEXAMPLES= example1.c example2.c example3.c example4.c seqio.c seqio.h Makefile
XPROGRAMS= fmtseq grepseq idxseq typeseq wcseq
X
Xdo-install:
X ${MKDIR} ${DOCSDIR}
X ${MKDIR} ${DOCSDIR}/html
X ${MKDIR} ${EXAMPLESDIR}
X cd ${WRKSRC}; \
X for file in ${PROGRAMS}; do \
X ${INSTALL_PROGRAM} $$file ${PREFIX}/bin; \
X done
X cd ${WRKSRC}; \
X for file in ${EXAMPLES}; do \
X ${INSTALL_DATA} $$file ${EXAMPLESDIR}; \
X done
X ${INSTALL_DATA} ${WRKSRC}/bioseq.txt ${DOCSDIR}
X cd ${WRKSRC}/doc; \
X for file in *.doc; do \
X ${INSTALL_DATA} $$file ${DOCSDIR}; \
X done
X cd ${WRKSRC}/html; \
X for file in *.html; do \
X ${INSTALL_DATA} $$file ${DOCSDIR}/html; \
X done
X
X.include <bsd.port.mk>
END-of-seqio/Makefile
exit
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