Subject: rev 7 - trunk/analyses

From: [email-masked]
Date: Thu, 8 Aug 2002 01:26:05 -0500

Author: kfogel
Date: Thu, 08 Aug 2002 01:26:00 -0500
New Revision: 7

Added:
   trunk/analyses/check-bases.in
Removed:
   trunk/analyses/check-bases.sh
Modified:
   trunk/analyses/Makefile.in
Log:
* analyses/check-bases.in: Replaces check-bases.sh.  This is the input
  file from which the check-bases program is generated, so it should
  follow the ".in" idiom.

* analyses/Makefile.in: Adjust accordingly.

Modified: trunk/analyses/Makefile.in
==============================================================================
--- trunk/analyses/Makefile.in	(original)
+++ trunk/analyses/Makefile.in	Thu Aug  8 01:26:04 2002
@@ -19,7 +19,7 @@
 # Where to put architecture-specific files, like utility executables 
 ARCHDIR=${LIBDIR}/${ARCHITECTURE}
 
-SOURCES = check-bases.sh check-tabl.c \
+SOURCES = check-bases.in check-tabl.c \
 	  count-tabl.c \
 	  lenstring.c lenstring.h \
 	  hash.h hash.c \
@@ -29,8 +29,8 @@
 
 all: ${EXECS}
 
-check-bases: check-bases.sh Makefile
-	sed < check-bases.sh > check-bases \
+check-bases: check-bases.in Makefile
+	sed < check-bases.in > check-bases \
 	-e 's:^ARCHDIR=.*$$:ARCHDIR="${ARCHDIR}":'
 	chmod a+x check-bases

Copied: check-bases.in (from rev 6, trunk/analyses/check-bases.sh)

Deleted: trunk/analyses/check-bases.sh
==============================================================================
--- trunk/analyses/check-bases.sh	(original)
+++ trunk/analyses/check-bases.sh	Thu Aug  8 01:26:04 2002
@@ -1,89 +0,0 @@
-#!/bin/sh
-#### check-bases --- check for changed bases between two alignments
-#### Jim Blandy <[email-masked]> --- November 1994
-
-progname="`echo $0 | sed -e 's:^.*/::'`"
-
-usage="Usage: ${progname} REFERENCE FILE ...
-Compare REFERENCE against each FILE; report changes to bases, and ignore gaps.
-Files may be GenBank, EMBL, FASTA, or RDP GDBM files."
-
-if [ $# = 0 ]; then
-  echo "${usage}" >&2
-  exit 1
-fi
-
-if [ $# = 1 ]; then
-  (echo "${progname}: Compare \`$1' against what?"
-   echo "${usage}") >&2
-  exit 1
-fi
-
-ARCHDIR=this is replaced by the directory containing the utility programs
-PATH="${ARCHDIR}:${PATH}"
-
-reference="$1" ; shift
-tmpref="/tmp/cbr-$$"
-tmpin="/tmp/cbi-$$"
-
-trap 'rm -rf ${tmpref} ${tmpin}' 0
-trap 'rm -rf ${tmpref} ${tmpin}; exit 1' 1 2 15
-
-if [ ! -r "${reference}" ]; then
-  echo "${progname}: reference file `${reference}' does not exist" >&2
-  exit 2
-fi
-
-case "$reference" in
-  *".gb" )
-    gb-tabl --annotation-out /dev/null < "${reference}" > "${tmpref}"
-  ;;
-  *".embl" )
-    embl-tabl --annotation-out /dev/null < "${reference}" > "${tmpref}"
-  ;;
-  *".fasta" )
-    fasta-tabl --annotation-out /dev/null < "${reference}" > "${tmpref}"
-  ;;
-  *".gdbm" )
-    gdbm -g "${reference}" --annotations /dev/null > "${tmpref}"
-  ;;
-  *".phy" )
-    phylip-tabl -t -f --annotations /dev/null < "${reference}" > "${tmpref}"
-  ;;
-  * )
-    echo "${progname}: don't recognize format of \`${reference}'" >&2
-    exit 2
-  ;;
-esac
-
-for file in "$@"; do
-
-  if [ ! -r "${file}" ]; then
-    echo "${progname}: comparison file `${file}' does not exist" >&2
-    exit 2
-  fi
-
-  case "$file" in
-    *".gb" )
-      gb-tabl --annotation-out /dev/null < "${file}" > "${tmpin}"
-    ;;
-    *".embl" )
-      embl-tabl --annotation-out /dev/null < "${file}" > "${tmpin}"
-    ;;
-    *".fasta" )
-      fasta-tabl --annotation-out /dev/null < "${file}" > "${tmpin}"
-    ;;
-    *".gdbm" )
-      gdbm -g "${file}" --annotations /dev/null > "${tmpin}"
-    ;;
-    *".phy" )
-      phylip-tabl -t -f --annotations /dev/null < "${file}" > "${tmpin}"
-    ;;
-    * )
-      echo "${progname}: don't recognize format of \`${file}'" >&2
-      exit 2
-    ;;
-  esac
-
-  check-tabl ${tmpref} -n "${reference}" ${tmpin} -n "${file}"
-done