26 lines
645 B
Bash
26 lines
645 B
Bash
#! /bin/bash
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <reliable_seq> <less_reliable_seq> <stem>"
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echo "Perform MACSE alignment on given sequences"
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exit 1
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fi
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seq=$1
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seq_lr=$2
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stem=$3
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{
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echo "Command:"
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echo "macse -prog alignSequences -seq $seq -seq_lr ${seq_lr}"
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echo " -out_NT ${stem}.nal -out_AA ${stem}.pal"
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echo " -optim 2 -max_refine_iter 3 -local_realign_init 0.2"
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} >alignSequences.log
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macse -prog alignSequences \
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-seq "$seq" -seq_lr "${seq_lr}" \
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-out_NT "$stem".nal -out_AA "$stem".pal \
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-optim 2 \
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-max_refine_iter 3 \
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-local_realign_init 0.2 \
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>>alignSequences.log 2>&1
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