run-mummer

#!/bin/bash

name=$1
i=$2
l=$3

echo "${name}: i${i}, l${l}"

if [[ ! -s ${name}-i${i}-l${l}.delta ]]; then
    echo "Filtering delta..."
    delta-filter -q -r -i ${i} -l ${l} ${name}.delta \
                 > ${name}-i${i}-l${l}.delta
fi

if [[ ! -s ${name}-i${i}-l${l}.coords ]]; then
    echo "Making coords..."
    show-coords -THrcl ${name}-i${i}-l${l}.delta \
                > ${name}-i${i}-l${l}.coords
fi

if [[ ! -s ${name}.lengths ]]; then
    echo "Getting scaffold lengths..."
    fastalength ${name}.fasta | sort -k2,2 > ${name}.lengths
fi

for chr in {01..12}; do
    echo "Doing chr ${chr}..."

    # find scaffold order and orientation
    awk '$12 == "ST4.03ch'${chr}'" {print $1,$2,$3,$4,$13;}' \
        ${name}-i${i}-l${l}.coords \
        | sort -n -k1,1 \
        | sort -s -k5 \
        | awk '
BEGIN {
   lastn=""; lastm=0; lastb=0; lastl=0;
} 
{
   n=$5; s=$1; e=$2; p=(s+e)/2; b=e-s; l=$4-$3;
   if (lastn=="") {
      lastn=n; lastm=p; lastb=b; lastl=l;
   } else if (lastn!=n) {
      print lastn,int(lastm),lastl
      lastn=n; lastm=p; lastb=b; lastl=l;
   } else {
      lastm=(lastm*lastb+p*b)/(lastb+b); lastb+=b; lastl+=l
   }
}
END {
   print lastn,int(lastm),lastl
}
' \
        | sort -k1,1 \
               > ${name}-chr${chr}-contigs-i${i}-l${l}.scaf-pos-orn

    join -1 1 -2 2 \
         ${name}-chr${chr}-contigs-i${i}-l${l}.scaf-pos-orn \
         ${name}.lengths \
        | sort -n -k2,2 \
        | awk '{if ($3>0) {sign="+"} else {sign="-"} printf "%s\t%d\t%s\n", $1, $4, sign;}' \
              > ${name}-chr${chr}-contigs-i${i}-l${l}.mumlist
    
    mummerplot -t png -r ST4.03ch${chr} -p ${name}-i${i}-l${l}-${chr} \
               ${name}-i${i}-l${l}.delta \
               -Q ${name}-chr${chr}-contigs-i${i}-l${l}.mumlist
done