Project 2: Step 2: Get S6 Genomes

## many files are available at this github repository
git clone https://github.com/csb5/hospital_microbiome.git
cd ./hospital_microbiome/output_tables
grep s6 strain_cluster_summary.tsv | grep Acinetobacter | grep -v s62| cut -f3 >../../s6.nanopore.ids
cd ../..
## genome files are available at figshare, we will grab some of them
wget https://ndownloader.figshare.com/files/21229971
tar -xvzf 21229971
## this will extract the tarball of hybrid assemblies to home/bertrandd/PROJECT_LINK/OPERA_LG/HOSPITAL_MICROBIOME/assembly_db//hybrid_assembly_genomes/
wget https://ndownloader.figshare.com/files/21229929
mv 21229929 hybrid_assembly_genome_info.tab
## use the list of nanopore ids from cluster s6 to obtain the genome ids
fgrep -f s6.nanopore.ids hybrid_assembly_genome_info.tab |  cut -f1 >s6.genome.ids
mkdir s6
## copy the genomes for cluster s6 to a new directory
for i in `cat s6.genome.ids`; do cp ./home/bertrandd/PROJECT_LINK/OPERA_LG/HOSPITAL_MICROBIOME/assembly_db/hybrid_assembly_genomes/$i.fa s6/. ; done