git://source.jalview.org
/
jalview.git
/ blob
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
history
|
raw
|
HEAD
JAL-2844 removed resetting line drawing to keep line on screen
[jalview.git]
/
forester
/
sh
/
x_mafft.sh
1
re="(.+)_ni\.fasta$"
2
#re="(.+)\.fasta$"
3
cutoff=3
4
for i in *
5
do
6
if test -f "$i"
7
then
8
if [[ $i =~ $re ]]
9
then
10
name=${BASH_REMATCH[1]}
11
echo $name
12
count=$(grep -c '>' $i)
13
echo $count
14
if [ $count -gt $cutoff ]
15
then
16
/usr/local/bin/mafft --maxiterate 1000 --localpair $i > ${name}_mafft_1000_l.fasta
17
rc=$?
18
if [[ $rc != 0 ]]
19
then
20
exit $rc
21
fi
22
fi
23
fi
24
fi
25
done