#!/bin/tcsh -f
#(ie run the tshell on this but don't read the .cshrc or .tcshrc)

echo version = 1.02 of mksequ 2006 Oct 26
# 2006 Oct 26, 1.02: better order
# 2006 Oct 26, 1.01: parsed ok
# 2006 Oct 26, 1.00: origin 

# make the sequences from the book.
# This requires identifying all the parts of the oligo and removing them.
# These parts are marked as break1 to break6.

set name = fur-oligos.book
cp ../$name book
parse

set break1 = "@OVERHANG-"
set break2 = "-@HAIRPIN-LARGE-"
set break3 = "-@HAIRPIN-SMALL-"
set break4 = "-END"
set break5 = "-@5CLAMP-"
set break6 = "-@3CLAMP"

set t1 = /tmp/furtable1-`whoami`
set t2 = /tmp/furtable2-`whoami`
set t3 = /tmp/furtable3-`whoami`
set t4 = /tmp/furtable4-`whoami`
set t5 = /tmp/furtable5-`whoami`

cat list |\
sed "s/^gcta/^$break1/" |\
#tr '.' '@' |\
#sed "s/cgcga@/$break6/" |\
tr '^' '\n' |\
cat > $t1

echo `grep ${break1} $t1 | wc -l` sequences found

echo ---- $t1
cat $t1
echo ----

# form the material into one single line:
cat $t1 |\
fmt -200 |\
tr -d ' ' |\
sed "s/\./$break4/" |\
cat > $t2

echo ---- $t2
cat $t2
echo ----

cat $t2 |\
sed "s/${break1}/${break1}^/" |\
sed "s/acgatcgcgcgaagcgcgatcgt/.^$break2/" |\
# introduce the period after the sequence \
# sed "s/gcgaagc/.^$break3/" |\ too small! \
sed "s/cgcgaagcg/.^$break3/" |\
sed "s/tcgcg/$break5^/" |\
sed "s/cgcga-/${break6}-/" |\
cat > $t3

echo ---- $t3
cat $t3
echo ----

cat $t3 |\
tr '^' '\n' |\
cat > $t4

echo ---- $t4 sesquence broken into parts
cat $t4
echo ----

cat $t4 |\
grep -v @ |\
noblank |\
cat > $t5

echo ---- $t5 natural sesquences, sequ
cat $t5
echo ----

cat $t5 >sequ

# **************************************************

cat ../makebkp |\
sed "s/furoligos/Natural Fur site sequences/" |\
cat > makebkp
cat makebkp
makebk < makebkp