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

input_prep/make_ss.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+# From: https://github.com/RosettaCommons/RoseTTAFold
+
+if [ -z  "${BLASTMAT}" ]; then
+    export BLASTMAT=$PIPE_DIR/blast-2.2.26/data/
+fi
+
+DATADIR="$CONDA_PREFIX/share/psipred_4.01/data"
+echo $DATADIR
+
+i_a3m="$1"
+o_ss="$2"
+
+ID=$(basename $i_a3m .a3m).tmp
+
+$PIPE_DIR/csblast-2.2.3/bin/csbuild -i $i_a3m -I a3m -D $PIPE_DIR/csblast-2.2.3/data/K4000.crf -o $ID.chk -O chk
+
+head -n 2 $i_a3m > $ID.fasta
+echo $ID.chk > $ID.pn
+echo $ID.fasta > $ID.sn
+
+makemat -P $ID
+psipred $ID.mtx $DATADIR/weights.dat $DATADIR/weights.dat2 $DATADIR/weights.dat3 > $ID.ss
+psipass2 $DATADIR/weights_p2.dat 1 1.0 1.0 $i_a3m.csb.hhblits.ss2 $ID.ss > $ID.horiz
+
+(
+echo ">ss_pred"
+grep "^Pred" $ID.horiz | awk '{print $2}'
+echo ">ss_conf"
+grep "^Conf" $ID.horiz | awk '{print $2}'
+) | awk '{if(substr($1,1,1)==">") {print "\n"$1} else {printf "%s", $1}} END {print ""}' | sed "1d" > $o_ss
+
+rm ${i_a3m}.csb.hhblits.ss2
+rm $ID.*