mmetsp_loops.sh

for file in $(find . -name "*.fasta.dammit.gff3"); do echo $file; cut -f1 $file | uniq | wc -l; done > ~/MMETSP/assembly_evaluation_data/total_contigs



for file in $(find `pwd` -name "*.fasta.renamed.fasta.dammit.gff3"); 
do 
  base=$(basename $file .renamed.fasta.dammit.gff3)
  new=$base.dammit.gff3
  echo cp $file /mnt/scratch/ljcohen/mmetsp_dammit/cp/gff3/$new 
done

for file in $(find `pwd` -name "*.fasta.renamed.fasta.dammit.fasta"); 
do 
  base=$(basename $file .renamed.fasta.dammit.fasta)
  new=$base.dammit.fasta
  echo cp $file /mnt/scratch/ljcohen/mmetsp_dammit/cp/fasta/$new 
done