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#! /bin/sh
#
# iterate_rates file_name_root program_options [cycles]
if test $# -lt 2; then
echo "Usage: iterate_rates file_name_root [cycles]";
exit
fi
root0="$1"
if test -f "${root0}.phylip"; then suf=phylip
elit test -f "${root0}.phy"; then suf=phy
else
echo "Could not find sequence file ${root0}.phy[lip]"
exit
fi
root=`echo "$root0" | sed 's&^.*/\([^/][^/]*\)$&\1&'`
if test $# -gt 2; then cycles=$3; else cycles=0; fi
tree1=`ls -1 ${root}_*.tree | tail -1`
if test -z "$tree1"; then
transition 2 < ${root}.$suf | treefile | quickadd | global 0 0 | fastDNAml >/dev/null
mv `ls -t treefile.*|head -1` "${root}.dummy_tree"
usertree "${root}.dummy_tree" < ${root0}.$suf | n_categories 35 | treefile | DNAml_rates > /dev/null
mv `ls -t treefile.*|head -1`
v0=0;
v1=1;
else
v0=`echo "$tree1" | sed 's/^.*_\([0-9][0-9]*)\.tree$/\1/'`
v1=`expr $v0 + 1`
fi
if test ! -f ${root}_${v0}.$suf; then ln -s ${root}.$suf ${root}_${v0}.$suf; fi
usertree $tree1 < ${root}_${v0}.$suf | n_categories 35 | treefile | frequencies | DNAml_rates > ${root}_${v0}.rates
mv weight_rate.* ${root}_${v0}.wr
if test ! -f ${root}_${v1}.$suf; then ln -s ${root}.$suf ${root}_${v1}.$suf; fi
fastDNAml_loop -m 20 ${root}_${v1}.$suf 3 "frequencies | weights_categories ${root}_${v0}.wr"
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