runSpruceView.sh

#!/bin/bash
#RLW 2017,2019
if [ $# -ne 11 ]; then
        echo "Usage: $(basename $0)"
        echo "  QUERY FASTA"
        echo "  REFERENCE/SUBJECT/TARGET FASTA"
        echo "  ALPHA TRANSPARENCY 0-255"
        echo "  MISMATCH THRESHOLD"
        echo "  BLOCK LENGTH (bp)"
        echo "  LABEL"
        echo "  SCALE (1:n)"
        echo "  QUERY features GFF .tsv"
        echo "  REFERENCE features GFF .tsv"
        echo "  cross_match/minimap2"
        echo "  PATH-TO-FONTS"
        exit 1
fi

echo Running: $(basename $0) $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11}


# source PATH-TO-SOURCE (IF NEEDED)

echo "Make sure xmatchview-conifer.py, cross_match and minimap2 are in your PATH"

if [ ${10} == 'cross_match' ]; then

   # cross_match pipeline
   cross_match $1 $2 -minmatch 5 -minscore 10 -masklevel 101 > $1_vs_$2.rep
   xmatchview-conifer.py -x $1_vs_$2.rep -q $1 -s $2 -a $3 -m $4 -b $5 -l $6 -c $7 -f png -y $8 -e $9 -p ${11}

elif [ ${10} == 'minimap2' ]; then

   # minimap pipeline
   minimap2 $2 $1 -N200 -p0.0001 > $1_vs_$2.paf
   xmatchview-conifer.py -x $1_vs_$2.paf -q $1 -s $2 -a $3 -m $4 -b $5 -l $6 -c $7 -f png -y $8 -e $9 -p ${11}

else

   echo Unrecognizable option ${10}
   echo Make sure you specify: cross_match OR minimap2

fi