SYNOPSIS autodoals [file.fa or file.blc] [no]
if "no" is specified in the command line, the output ill be in black and white.

[dcoop Coms]-> cat autodoals
#!/bin/sh
if [ $1 ]; then file=$1
 else echo "Please pick a .fa or .blc file.  These are available:"
 echo ; ls *.fa *.blc; echo ; echo -n "Which one?  " ;read file
fi
if [ $2 = "no" ]; then color=no; else color=yes; fi

name=`echo $file |awk -F . '{print ($1)}'`
ext=`echo $file |awk -F . '{print ($NF)}'`

if [ $ext == "fa" ] ; then
 clustalw -align -outorder=input -infile=$file -output=gcg
 msf2blc -q < $name.msf > tEmP
 sed '/iteration/,/endoffile/ s/\./ /g' tEmP > $name.blc
 rm -f tEmP
fi

#Use this section to describe what goes on what line
nb=2                 # number of lines before sequences
na=5                 # number of lines after sequences
gap=.                # Gap character
indent=6            # Indent width

# Necessary Calculations -- no changes should be necessary
ns=`grep -c ">" $name.blc`        # number of seqs
fs=`expr $nb + 1`                 # line of first sequence
ls=`expr $nb + $ns`               # line of last sequence
ab=`grep -n "*" $name.blc |head -1 |awk -F ":" '{print $1}'`
ae=`grep -n "*" $name.blc |tail -1 |awk -F ":" '{print $1}'`
loa=`expr  $ae - $ab - 1`         #Length of alignment
#nc defines the percentage of conservation
nc=`expr $ns \* 6 / 10`

#Generate Alscript Input
cat << end-als > temp.als
     #Comments in ALscript command files start with a #
     #Commands are free format - separated by blank, tab or comma characters
     #But no blank lines.  Blank lines must have a comment character #
     #
     BLOCK_FILE         $name.blc
     OUTPUT_FILE        $name.ps
     PORTRAIT
     #LANDSCAPE
     #	MAX_SIDE 8.3
     POINTSIZE 7
     DEFINE_FONT 0 Helvetica DEFAULT
     DEFINE_FONT 1 Helvetica-Bold DEFAULT
     DEFINE_FONT 2 Helvetica REL .2
     DEFINE_FONT 3 Symbol REL 1.2
     DEFINE_FONT 4 Courier-Bold DEFAULT
     IDENT_WIDTH $indent
     ADD_SEQ 0 $nb
     ADD_SEQ $ns $na
SINGLE_PAGE
  bw#DEFINE_COLOUR 1 .2 .2 .2
  bw#DEFINE_COLOUR 2 .4 .4 .4
  bw#DEFINE_COLOUR 3 .8 .8 .8
 col#DEFINE_COLOUR 1 1 0 0
 col#DEFINE_COLOUR 2 0 0 1
 col#DEFINE_COLOUR 3 0 1 0
 col#DEFINE_COLOUR 4 0 1 1
 col#DEFINE_COLOUR 5 1 0 1
 col#DEFINE_COLOUR 6 1 .4 .4
 col#DEFINE_COLOUR 7 .4 .4 1
 col#DEFINE_COLOUR 8 .4  1 .4
  #   NUMBER_SEQS
     DO_TICKS
  #   NO_NUMBERS
     SETUP              #Tell the program to get on with the formatting.
     ID_FONT ALL 4
FONT_REGION ALL 1
FONT_REGION 1 $fs $loa $ls 0
     RELATIVE_TO $fs 1  #assumes your sequence on top
     #
#Mask for conservative substitution
  #Calculate Mask
     #  Next line assumes your sequence is on top of the alignment
     RELATIVE_TO 0
     SUB_CHARS 1 $fs $loa $ls SPACE "$gap" 
     #  Mask for conserved
     calcons  1 $fs $loa $ls
  #Draw Mask -- 
  # Black text with green background
  #Last number on next line is % conserved  (times ten) for conservative sub
     mask SETUP
     mask CONSERVATION 1 $fs $loa $ls 6
     mask CCOL 1 $fs $loa $ls 100
     mask FONT 1 $fs $loa $ls 1
     mask SCOL 1 $fs $loa $ls 3
     mask RESET
#
#This mask is for X % IDENTICAL 
#  White text on blue background
# X is defined by nc above
#Last number on next line is #/total seqs for conserved
     mask SETUP
     mask ILLEGAL "$gap"
     mask  ID 1 $fs $loa $ls $nc 
     mask SCOL 1 $fs $loa $ls 2
     mask CCOL 1 $fs $loa $ls 99 
     mask FONT 1 $fs $loa $ls 1
     mask RESET
#Mask for total identity
     mask CONSERVATION 1 $fs $loa $ls 10 
 col#mask SCOL 1 $fs $loa $ls 1
  bw#mask SCOL 1 $fs $loa $ls 100
     mask CCOL 1 $fs $loa $ls 99
    # mask FONT 1 $fs $loa $ls 1
     mask RESET
     # End of Alscript input file
end-als

if [ $color == "yes" ] ; then grep -v "bw#" temp.als | sed 's/col#/    /g' > $name.als
 else grep -v "col#" temp.als | sed 's/bw#/   /g' > $name.als
fi
alscript $name.als > $name.ps 
kghostview $name.ps &
#gs -dBATCH -dNOPAUSE -sDEVICE=jpeg -sOutputFile=$name.jpg -r100 $name.ps