# renum.sh   Renumbers a bunch of sequences
# that are already formatted.  Skips lines that don't begin with %

# First argument is input file name, second is first free A-number

# Note to myself: remember to maintain the link
# ln renum.sh /usr/njas/wwwfiles/sequences/renum.sh.txt

# If you download this from my web page, it is important to
# use the SOURCE FILE.  DON'T mouse it off the screen
# because many of the characters will not be visible.

# Call this file  renum.sh (not renum.sh.txt)

# Corrected Nov 19 2002
# Modified Nov 02, 2002
# Modified Oct 08, 1999.

# Set version of awk to use:
AWK=/bin/gawk

if [ "$#" -ne 2 ]
then
echo "Incorrect no of arguments. Usage: renum.sh infile 14376 >out "
exit 1
fi

$AWK ' BEGIN { at = '$2' - 1 }

$1 ~ /%I/ { printf("\n");
    at = at + 1 ;
# Pad length of at to 6 digits
    t1 = at
    while ( length(t1) < 6 )
	t1 = 0 t1
    t2 = "A" t1 }

$0 ~ /^%/ { sub($2, t2); print }

      END { printf("\n")}  ' $1 | sed '1d'