CREGEX problems with PROSITE.DAT

Lee F. Kolakowski lfk at eastman1.mit.edu
Sat Oct 24 15:27:19 EST 1992


On 23 Oct 92 18:33:57 GMT,
lapointe at THORIN.UTHSCSA.EDU ("David Lapointe") said:
> I have been trying to use CREGEX to reformat prosite.dat to prosite.regex
> for use with the PROSEARCH AWK software.

> Has anyone else encountered this problem? Solutions?

That has been fixed and here is a new version
Look for a discription of the program in December 1992  BioTechniques.

#! /bin/sh
# This is a shell archive.  Remove anything before this line, then unpack
# it by saving it into a file and typing "sh file".  To overwrite existing
# files, type "sh file -c".  You can also feed this as standard input via
# unshar, or by typing "sh <file", e.g..  If this archive is complete, you
# will see the following message at the end:
#		"End of shell archive."
# Contents:  ProSearch2.1 ProSearch2.1/COPYING ProSearch2.1/INSTALL
#   ProSearch2.1/MISSING.regex ProSearch2.1/Makefile
#   ProSearch2.1/README_V1 ProSearch2.1/README_V2.1
#   ProSearch2.1/cregex_ansi.c ProSearch2.1/cregex_sun.c
#   ProSearch2.1/prodoc.awk ProSearch2.1/prosearc.bat
#   ProSearch2.1/prosearch.1 ProSearch2.1/prosearch.help
#   ProSearch2.1/prosearch.orig ProSearch2.1/prosite.awk
#   ProSearch2.1/regex_update.orig ProSearch2.1/test.out
#   ProSearch2.1/test.pep
# Wrapped by lfk at eastman1 on Sat Sep 26 20:10:04 1992
PATH=/bin:/usr/bin:/usr/ucb ; export PATH
if test ! -d 'ProSearch2.1' ; then
    echo shar: Creating directory \"'ProSearch2.1'\"
    mkdir 'ProSearch2.1'
fi
if test -f 'ProSearch2.1/COPYING' -a "${1}" != "-c" ; then 
  echo shar: Will not clobber existing file \"'ProSearch2.1/COPYING'\"
else
echo shar: Extracting \"'ProSearch2.1/COPYING'\" \(12488 characters\)
sed "s/^X//" >'ProSearch2.1/COPYING' <<'END_OF_FILE'
X
X		    GNU GENERAL PUBLIC LICENSE
X		     Version 1, February 1989
X
X Copyright (C) 1989 Free Software Foundation, Inc.
X                    675 Mass Ave, Cambridge, MA 02139, USA
X Everyone is permitted to copy and distribute verbatim copies
X of this license document, but changing it is not allowed.
X
X			    Preamble
X
X  The license agreements of most software companies try to keep users
Xat the mercy of those companies.  By contrast, our General Public
XLicense is intended to guarantee your freedom to share and change free
Xsoftware--to make sure the software is free for all its users.  The
XGeneral Public License applies to the Free Software Foundation's
Xsoftware and to any other program whose authors commit to using it.
XYou can use it for your programs, too.
X
X  When we speak of free software, we are referring to freedom, not
Xprice.  Specifically, the General Public License is designed to make
Xsure that you have the freedom to give away or sell copies of free
Xsoftware, that you receive source code or can get it if you want it,
Xthat you can change the software or use pieces of it in new free
Xprograms; and that you know you can do these things.
X
X  To protect your rights, we need to make restrictions that forbid
Xanyone to deny you these rights or to ask you to surrender the rights.
XThese restrictions translate to certain responsibilities for you if you
Xdistribute copies of the software, or if you modify it.
X
X  For example, if you distribute copies of a such a program, whether
Xgratis or for a fee, you must give the recipients all the rights that
Xyou have.  You must make sure that they, too, receive or can get the
Xsource code.  And you must tell them their rights.
X
X  We protect your rights with two steps: (1) copyright the software, and
X(2) offer you this license which gives you legal permission to copy,
Xdistribute and/or modify the software.
X
X  Also, for each author's protection and ours, we want to make certain
Xthat everyone understands that there is no warranty for this free
Xsoftware.  If the software is modified by someone else and passed on, we
Xwant its recipients to know that what they have is not the original, so
Xthat any problems introduced by others will not reflect on the original
Xauthors' reputations.
X
X  The precise terms and conditions for copying, distribution and
Xmodification follow.
X
X		    GNU GENERAL PUBLIC LICENSE
X   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
X
X  0. This License Agreement applies to any program or other work which
Xcontains a notice placed by the copyright holder saying it may be
Xdistributed under the terms of this General Public License.  The
X"Program", below, refers to any such program or work, and a "work based
Xon the Program" means either the Program or any work containing the
XProgram or a portion of it, either verbatim or with modifications.  Each
Xlicensee is addressed as "you".
X
X  1. You may copy and distribute verbatim copies of the Program's source
Xcode as you receive it, in any medium, provided that you conspicuously and
Xappropriately publish on each copy an appropriate copyright notice and
Xdisclaimer of warranty; keep intact all the notices that refer to this
XGeneral Public License and to the absence of any warranty; and give any
Xother recipients of the Program a copy of this General Public License
Xalong with the Program.  You may charge a fee for the physical act of
Xtransferring a copy.
X
X  2. You may modify your copy or copies of the Program or any portion of
Xit, and copy and distribute such modifications under the terms of Paragraph
X1 above, provided that you also do the following:
X
X    a) cause the modified files to carry prominent notices stating that
X    you changed the files and the date of any change; and
X
X    b) cause the whole of any work that you distribute or publish, that
X    in whole or in part contains the Program or any part thereof, either
X    with or without modifications, to be licensed at no charge to all
X    third parties under the terms of this General Public License (except
X    that you may choose to grant warranty protection to some or all
X    third parties, at your option).
X
X    c) If the modified program normally reads commands interactively when
X    run, you must cause it, when started running for such interactive use
X    in the simplest and most usual way, to print or display an
X    announcement including an appropriate copyright notice and a notice
X    that there is no warranty (or else, saying that you provide a
X    warranty) and that users may redistribute the program under these
X    conditions, and telling the user how to view a copy of this General
X    Public License.
X
X    d) You may charge a fee for the physical act of transferring a
X    copy, and you may at your option offer warranty protection in
X    exchange for a fee.
X
XMere aggregation of another independent work with the Program (or its
Xderivative) on a volume of a storage or distribution medium does not bring
Xthe other work under the scope of these terms.
X
X  3. You may copy and distribute the Program (or a portion or derivative of
Xit, under Paragraph 2) in object code or executable form under the terms of
XParagraphs 1 and 2 above provided that you also do one of the following:
X
X    a) accompany it with the complete corresponding machine-readable
X    source code, which must be distributed under the terms of
X    Paragraphs 1 and 2 above; or,
X
X    b) accompany it with a written offer, valid for at least three
X    years, to give any third party free (except for a nominal charge
X    for the cost of distribution) a complete machine-readable copy of the
X    corresponding source code, to be distributed under the terms of
X    Paragraphs 1 and 2 above; or,
X
X    c) accompany it with the information you received as to where the
X    corresponding source code may be obtained.  (This alternative is
X    allowed only for noncommercial distribution and only if you
X    received the program in object code or executable form alone.)
X
XSource code for a work means the preferred form of the work for making
Xmodifications to it.  For an executable file, complete source code means
Xall the source code for all modules it contains; but, as a special
Xexception, it need not include source code for modules which are standard
Xlibraries that accompany the operating system on which the executable
Xfile runs, or for standard header files or definitions files that
Xaccompany that operating system.
X
X  4. You may not copy, modify, sublicense, distribute or transfer the
XProgram except as expressly provided under this General Public License.
XAny attempt otherwise to copy, modify, sublicense, distribute or transfer
Xthe Program is void, and will automatically terminate your rights to use
Xthe Program under this License.  However, parties who have received
Xcopies, or rights to use copies, from you under this General Public
XLicense will not have their licenses terminated so long as such parties
Xremain in full compliance.
X
X  5. By copying, distributing or modifying the Program (or any work based
Xon the Program) you indicate your acceptance of this license to do so,
Xand all its terms and conditions.
X
X  6. Each time you redistribute the Program (or any work based on the
XProgram), the recipient automatically receives a license from the original
Xlicensor to copy, distribute or modify the Program subject to these
Xterms and conditions.  You may not impose any further restrictions on the
Xrecipients' exercise of the rights granted herein.
X
X  7. The Free Software Foundation may publish revised and/or new versions
Xof the General Public License from time to time.  Such new versions will
Xbe similar in spirit to the present version, but may differ in detail to
Xaddress new problems or concerns.
X
XEach version is given a distinguishing version n



More information about the Bio-soft mailing list