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@myleott
Created January 9, 2019 15:05
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#!/bin/bash
GEN=$1
SYS=$GEN.sys
REF=$GEN.ref
grep ^H $GEN | cut -f3- | perl -ple 's{(\S)-(\S)}{$1 ##AT##-##AT## $2}g' > $SYS
grep ^T $GEN | cut -f2- | perl -ple 's{(\S)-(\S)}{$1 ##AT##-##AT## $2}g' > $REF
python score.py --sys $SYS --ref $REF
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