Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

make_msa.sh

@@ -0,0 +1,134 @@
+#!/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 $SCRIPT`
+
+# sequence databases
+if [ -z  "${DB_UR30}" ]; then
+    DB_UR30="$PIPE_DIR/UniRef30_2020_06/UniRef30_2020_06"
+else
+    DB_UR30=$DB_UR30
+fi
+
+if [ -z  "${DB_BFD}" ]; then
+    DB_BFD="$PIPE_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
+else
+    DB_BFD=$DB_BFD
+fi
+
+# 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