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|
#! /bin/sh
# This generates text documentation from subset seeds.
cat <<'EOF'
LAST seeding schemes
====================
LAST's critical first step is to find *seeds*, i.e. initial matches
between query and reference sequences. It can use various seeding
schemes, which allow different kinds of mismatches at different seed
positions.
.. Note::
A seeding scheme consists of a seed alphabet, such as::
1 A C G T
0 ACGT
T AG CT
and one or more patterns, such as this one::
1T1T10T1101101
Each symbol in a pattern represents a grouping of sequence letters:
in this example, ``T`` represents the grouping ``AG CT``. At each
position in an initial match, mismatches are allowed between
letters that are grouped at that position in the pattern.
Although the patterns have fixed lengths, LAST's initial matches do
not. LAST finds shorter matches by using a prefix of the pattern,
and longer matches by cyclically repeating the pattern.
EOF
for i in "$@"
do
name=$(basename $i .seed)
echo $name
echo $name | sed 's/./-/g' # underline
echo
grep '^# ' $i | cut -d' ' -f2-
echo It uses this seed alphabet::
echo
awk '!/^#/ && NF > 1' $i | sed 's/^/ /'
echo
if [ $(awk 'NF == 1' $i | wc -l) = 1 ]
then echo And this pattern::
else echo And these patterns::
fi
echo
awk 'NF == 1' $i | sed 's/^/ /'
echo
grep -q '^#lastdb' $i && {
echo It sets this lastdb default:
grep '^#lastdb' $i | cut -d' ' -f2-
echo
}
grep -q '^#lastal' $i && {
echo It sets this lastal default:
grep '^#lastal' $i | cut -d' ' -f2-
echo
}
done
exit 0
|
