dna-diff-bestcontigs

#!/bin/bash

set -e

coords=$1
fasta=$2



cut -f 5,12,13 ${coords} \
    | sort -nr -k1,1 \
    | sort -s -k2,2 \
    | awk '$1 > 10000 {print $3}' \
    | sort \
    | uniq \
          > $(basename ${coords} .1coords).1contigs

while read seq; do
    ~/code/tools/fasta-index-get.py ${fasta} "^${seq}$"
done \
    < $(basename ${coords} .1coords).1contigs \
    > $(basename ${coords} .1coords).1contigs.fasta