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32 lines
875 B
Bash
32 lines
875 B
Bash
#!/bin/bash
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# From: https://github.com/RosettaCommons/RoseTTAFold
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export BLASTMAT=$PIPE_DIR/blast-2.2.26/data/
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DATADIR="$CONDA_PREFIX/share/psipred_4.01/data"
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echo $DATADIR
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i_a3m="$1"
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o_ss="$2"
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ID=$(basename $i_a3m .a3m).tmp
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$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
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head -n 2 $i_a3m > $ID.fasta
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echo $ID.chk > $ID.pn
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echo $ID.fasta > $ID.sn
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makemat -P $ID
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psipred $ID.mtx $DATADIR/weights.dat $DATADIR/weights.dat2 $DATADIR/weights.dat3 > $ID.ss
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psipass2 $DATADIR/weights_p2.dat 1 1.0 1.0 $i_a3m.csb.hhblits.ss2 $ID.ss > $ID.horiz
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(
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echo ">ss_pred"
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grep "^Pred" $ID.horiz | awk '{print $2}'
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echo ">ss_conf"
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grep "^Conf" $ID.horiz | awk '{print $2}'
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) | awk '{if(substr($1,1,1)==">") {print "\n"$1} else {printf "%s", $1}} END {print ""}' | sed "1d" > $o_ss
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rm ${i_a3m}.csb.hhblits.ss2
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rm $ID.*
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