Update 2.2.3_visualizing_taxonomy.md

_episodes/2.2.3_visualizing_taxonomy.md

@@ -318,25 +318,30 @@ with open(graph_filename) as json_file:
 > #SBATCH --mem=5G
 > #SBATCH --time=00:10:00
 > #SBATCH --job-name=taxonomic_graph
-> #SBATCH --output=30_results_taxonomic_graph/taxonomic_graph.slurm.%j.out
-> #SBATCH --error=30_results_taxonomic_graph/taxonomic_graph.slurm.%j.err
+> #SBATCH --output=./2.2_taxonomy/40_plot_networks/taxonomic_graph.slurm.%j.out
+> #SBATCH --error=./2.2_taxonomy/40_plot_networks/taxonomic_graph.slurm.%j.err
 > 
 > # activate the python virtual environment with the packages we need
 > source ../py3env/bin/activate
 > 
 > # in this sbatch script, its not necessarry to create the directory,
 > # we already told sbatch to create it for the log files.
-> mkdir -p 30_results_taxonomic_graph
+> mkdir -p ./2.2_taxonomy/40_plot_networks/
 > 
 > # define an array with contig ids to plot
 > declare -a arr=("contig_10" "contig_109", "contig_164")
-> 
+>
 > # loop through the array
 > for contig in "${arr[@]}"
 > do
-> 	# run our script for plotting the network around a contig of choice
-> 	python 30_taxonomic_graph.py ../2.2_viral_taxonomy/02_vcontact3_results_new_contig_names/graph.cyjs 30_results_taxonomic_graph/"$contig"_graph.png $contig
+> 	# run our scripts for plotting the network around a contig of choice
+>   # PLOT CONTIG IN LOCAL GENE SHARING NETWORK
+> 	python python_scripts/taxonomy/30_taxonomic_graph_local.py ../2.2_viral_taxonomy/02_vcontact3_results_new_contig_names/graph.cyjs ./2.2_taxonomy/40_plot_networks/"$contig"_graph_local.png $contig
+>
+>   # PLOT CONTIG IN GLOBAL GENE SHARING NETWORK
+>   python python_scripts/taxonomy/30_taxonomic_graph_global.py ../2.2_viral_taxonomy/02_vcontact3_results_new_contig_names/graph.cyjs ./2.2_taxonomy/40_plot_networks/"$contig"_graph_global.png $contig
 > done
+>
 > 
 > # deactivate the environment
 > deactivate