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Create make_ss.sh

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Alex Morehead 2024-03-10 14:45:48 -05:00 committed by GitHub
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commit 64228a4ac8
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#!/bin/bash
# From: https://github.com/RosettaCommons/RoseTTAFold
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.*