mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-09-15 22:08:31 +00:00
126 lines
4.2 KiB
Bash
Executable file
126 lines
4.2 KiB
Bash
Executable file
#!/bin/bash
|
|
|
|
# inputs
|
|
in_fasta="$1"
|
|
out_dir="$2"
|
|
|
|
# resources
|
|
CPU="$3"
|
|
MEM="$4"
|
|
|
|
# template database
|
|
DB_TEMPL="$5"
|
|
|
|
# current script directory (i.e., pipe directory)
|
|
SCRIPT=`realpath -s $0`
|
|
export PIPE_DIR=`dirname $SCRIPT`
|
|
|
|
# sequence databases
|
|
DB_UR30="$PIPE_DIR/UniRef30_2020_06/UniRef30_2020_06"
|
|
DB_BFD="$PIPE_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
|
|
|
|
# Running signalP 6.0
|
|
mkdir -p $out_dir/signalp
|
|
tmp_dir="$out_dir/signalp"
|
|
signalp6 --fastafile $in_fasta --organism other --output_dir $tmp_dir --format none --mode slow
|
|
trim_fasta="$tmp_dir/processed_entries.fasta"
|
|
if [ ! -s $trim_fasta ] # empty file -- no signal P
|
|
then
|
|
trim_fasta="$in_fasta"
|
|
fi
|
|
|
|
# setup hhblits command
|
|
export HHLIB=/software/hhsuite/build/bin/
|
|
export PATH=$HHLIB:$PATH
|
|
HHBLITS_UR30="hhblits -o /dev/null -mact 0.35 -maxfilt 100000000 -neffmax 20 -cov 25 -cpu $CPU -nodiff -realign_max 100000000 -maxseq 1000000 -maxmem $MEM -n 4 -d $DB_UR30"
|
|
HHBLITS_BFD="hhblits -o /dev/null -mact 0.35 -maxfilt 100000000 -neffmax 20 -cov 25 -cpu $CPU -nodiff -realign_max 100000000 -maxseq 1000000 -maxmem $MEM -n 4 -d $DB_BFD"
|
|
|
|
mkdir -p $out_dir/hhblits
|
|
tmp_dir="$out_dir/hhblits"
|
|
out_prefix="$out_dir/t000_"
|
|
|
|
# perform iterative searches against UniRef30
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
prev_a3m="$trim_fasta"
|
|
for e in 1e-10 1e-6 1e-3
|
|
do
|
|
echo "Running HHblits against UniRef30 with E-value cutoff $e"
|
|
if [ ! -s $tmp_dir/t000_.$e.a3m ]
|
|
then
|
|
$HHBLITS_UR30 -i $prev_a3m -oa3m $tmp_dir/t000_.$e.a3m -e $e -v 0
|
|
fi
|
|
hhfilter -maxseq 100000 -id 90 -cov 75 -i $tmp_dir/t000_.$e.a3m -o $tmp_dir/t000_.$e.id90cov75.a3m
|
|
hhfilter -maxseq 100000 -id 90 -cov 50 -i $tmp_dir/t000_.$e.a3m -o $tmp_dir/t000_.$e.id90cov50.a3m
|
|
prev_a3m="$tmp_dir/t000_.$e.id90cov50.a3m"
|
|
n75=`grep -c "^>" $tmp_dir/t000_.$e.id90cov75.a3m`
|
|
n50=`grep -c "^>" $tmp_dir/t000_.$e.id90cov50.a3m`
|
|
|
|
if ((n75>2000))
|
|
then
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
cp $tmp_dir/t000_.$e.id90cov75.a3m ${out_prefix}.msa0.a3m
|
|
break
|
|
fi
|
|
elif ((n50>4000))
|
|
then
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
cp $tmp_dir/t000_.$e.id90cov50.a3m ${out_prefix}.msa0.a3m
|
|
break
|
|
fi
|
|
else
|
|
continue
|
|
fi
|
|
done
|
|
|
|
# perform iterative searches against BFD if it failes to get enough sequences
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
e=1e-3
|
|
echo "Running HHblits against BFD with E-value cutoff $e"
|
|
if [ ! -s $tmp_dir/t000_.$e.bfd.a3m ]
|
|
then
|
|
$HHBLITS_BFD -i $prev_a3m -oa3m $tmp_dir/t000_.$e.bfd.a3m -e $e -v 0
|
|
fi
|
|
hhfilter -maxseq 100000 -id 90 -cov 75 -i $tmp_dir/t000_.$e.bfd.a3m -o $tmp_dir/t000_.$e.bfd.id90cov75.a3m
|
|
hhfilter -maxseq 100000 -id 90 -cov 50 -i $tmp_dir/t000_.$e.bfd.a3m -o $tmp_dir/t000_.$e.bfd.id90cov50.a3m
|
|
prev_a3m="$tmp_dir/t000_.$e.bfd.id90cov50.a3m"
|
|
n75=`grep -c "^>" $tmp_dir/t000_.$e.bfd.id90cov75.a3m`
|
|
n50=`grep -c "^>" $tmp_dir/t000_.$e.bfd.id90cov50.a3m`
|
|
|
|
if ((n75>2000))
|
|
then
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
cp $tmp_dir/t000_.$e.bfd.id90cov75.a3m ${out_prefix}.msa0.a3m
|
|
fi
|
|
elif ((n50>4000))
|
|
then
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
cp $tmp_dir/t000_.$e.bfd.id90cov50.a3m ${out_prefix}.msa0.a3m
|
|
fi
|
|
fi
|
|
fi
|
|
|
|
if [ ! -s ${out_prefix}.msa0.a3m ]
|
|
then
|
|
cp $prev_a3m ${out_prefix}.msa0.a3m
|
|
fi
|
|
fi
|
|
|
|
echo "Running PSIPRED"
|
|
mkdir -p $out_dir/log
|
|
$PIPE_DIR/input_prep/make_ss.sh $out_dir/t000_.msa0.a3m $out_dir/t000_.ss2 > $out_dir/log/make_ss.stdout 2> $out_dir/log/make_ss.stderr
|
|
|
|
if [ ! -s $out_dir/t000_.hhr ]
|
|
then
|
|
echo "Running hhsearch"
|
|
HH="hhsearch -b 50 -B 500 -z 50 -Z 500 -mact 0.05 -cpu $CPU -maxmem $MEM -aliw 100000 -e 100 -p 5.0 -d $DB_TEMPL"
|
|
|
|
cat $out_dir/t000_.ss2 $out_dir/t000_.msa0.a3m > $out_dir/t000_.msa0.ss2.a3m
|
|
$HH -i $out_dir/t000_.msa0.ss2.a3m -o $out_dir/t000_.hhr -atab $out_dir/t000_.atab -v 0
|
|
fi
|