I have the following script:
#!/bin/sh
# Use the PhiPack software on our two aligned sets of sequences...
mkdir FcFeABC
cd FcFeABC
../bin/PhiPack/Phi -f ../../Data/Real_Sequences_and_Networks/FcFeABC_alignment.fas -o -v -w 10 -g
cd -
mkdir FcL10
cd FcL10
../bin/PhiPack/Phi -f ../../Data/Real_Sequences_and_Networks/FcL10_alignment.fas -o -v -w 10 -g
cd -
# Use the PhiPack software on the simulated Datasets...
cd ../Data/Simulated_Sequences_and_Networks/Constant_Sex/Theta\ =\ 0.066/Theta\ =\ 0.066/Medium/CutSequences/;
rmus=($(ls -d *.fas))
cd -
absfiles=(../Data/Simulated_Sequences_and_Networks/Constant_Sex/Theta\ =\ 0.066/Theta\ =\ 0.066/Medium/CutSequences/*.fas)
if [ ${#rmus[@]} = ${#absfiles[@]} ]
then
mkdir ${rmus[@]}
for ((i=0; i<${#absfiles[@]}; i++));
do
cd ${rmus[$i]}
.../bin/PhiPack/Phi -f ${absfiles[$i]} -o -v -w 10 -g
cd -
done
else
echo "Error, Number of files created and files to be read differs"
fi
Which hit's an error at line 16:
./runPhiTests.sh: 16: ./runPhiTests.sh: Syntax error: "(" unexpected
Which is this line:
rmus=($(ls -d *.fas))
I don't understand why the '(' is unexpected - it's a simple assignment of the results of ls to an array.
Thanks, Ben W.
