27 lines
760 B
Bash
Executable File
27 lines
760 B
Bash
Executable File
#! /bin/bash
|
|
set -e
|
|
THREADS=${THREADS:-12}
|
|
|
|
if [ "$#" -ne 3 ]; then
|
|
echo "Usage: $0 <aln_dir> <out_dir> <ext>"
|
|
echo "Build FastTree phylogenetic trees and perform TreeShrink on trimmed MACSE nucleotide alignments"
|
|
exit 1
|
|
fi
|
|
|
|
aln_dir=$(readlink -f "$1")
|
|
out_dir=$(readlink -f "$2")
|
|
ext=$3
|
|
|
|
# fasttree
|
|
mkdir -p "$out_dir"
|
|
echo -n >fasttree.cmds
|
|
for i in "$aln_dir"/*."$ext"; do
|
|
j=$(basename "$i" ."$ext")
|
|
mkdir -p "$out_dir"/"${j}"
|
|
cp -s "$i" "$out_dir"/"${j}"/input.fasta
|
|
echo "FastTree -nt -gtr -quiet $out_dir/${j}/input.fasta > $out_dir/${j}/input.tree" >>fasttree.cmds
|
|
done
|
|
xargs -t -P "$THREADS" -I cmd -a fasttree.cmds bash -c "cmd"
|
|
# treeshrink
|
|
run_treeshrink.py -f -i "$out_dir"/ -t input.tree -a input.fasta >treeshrink.log
|