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

echo version = 1.01 of mktable 2006 Oct 27
# 2006 Oct 27, 1.01: add url
# 2006 Oct 26, 1.00: origin 

set tomdate = `tomdate`

set table = furoligos.tex
set parsed = parsed.list
set namelist = namelist

set t0 = /tmp/mktable0`whoami`
set t1 = /tmp/mktable1`whoami`
set t2 = /tmp/mktable2`whoami`
set t3 = /tmp/mktable3`whoami`

parse
cat list > $parsed
cat $parsed

echo;
echo "------ step 0: parse the accession";
echo;

set line = `head -3 $parsed | tail -1`
set accession = `echo $line[5]|sed "s/_/\\\\_/g"`
echo $accession

echo;
echo ------ step 1;
echo;

# number < list

cat $parsed |\
tail +3 |\
cat > $t1

cat $t1

echo; echo ------ step 2; echo;

cat $t1 |\
# make space between the sequences while removing 'piece number: ' \
sed 's/piece number: /@/' | tr '@' '\n' |\
# remove the number: \
sed 's/begin: /%@/' | tr '@' '\n' |\
grep -v '%' |\
# make each a single line: \
fmt -200 |\
sed 's/end:/\&/' |\
sed "s/length:/\&/" |\
sed "s/bases  linear/\&/" |\
noblank |\
sed 's/$/ \\\\/' |\
cat > $t2
cat $t2

echo; echo ------ step 3; echo;
paste $namelist $t2 |\
# change the tab to &: \
tr '	' '&' |\
# make the emph \
sed 's/&/} & /' |\
sed 's/^/\\emph{/' |\
cat > $t3
cat $t3

echo; echo ------ step 4; echo;

# header stuff
cat > $table << EOF
\begin{table}
\begin{tabular}{lllcl}
\hline
Name & Begin  & End    & Length  & Sequence     \\\\
     & (base) & (base) & (bases) & (\$5'\$ to \$3'\$) \\\\
\hline
EOF

cat $t3 >> $table


# tail stuff
cat >> $table << EOF
\hline
\end{tabular}
\caption{Sequences of natural Fur sites used for oligo constructions.}
The sequence is from \emph{E. coli} K12,
GenBank Accession $accession.
See Materials and Methods
for how these sequences were used.
Sequence walker analysis of the oligos is available at
% https://alum.mit.edu/www/toms/papers/fur/.
{\texttt{https://alum.mit.edu/www/\$\sim\$toms/papers/fur/}}.
% $table generated at $tomdate
\end{table}
EOF

echo ------- $table
cat $table
echo -------

cd latex
 l > /dev/null
cd ..

echo ------- release

cp $table /tmp/$table
chmod a+r /tmp/$table

echo ---------------
echo $table generated at $tomdate

exit
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