Update 2.1.2_host_prediction_II.md

Author: maltesie

_episodes/2.1.2_host_prediction_II.md

@@ -227,25 +227,26 @@ Finally, we will combine the results from RaFAH and BLAST to compare the two met
 > #SBATCH --mem=50G
 > #SBATCH --time=02:00:00
 > #SBATCH --job-name=rafah
-> #SBATCH --output=./2.1_host_prediction/10_rafah/rafah.slurm.%j.out
-> #SBATCH --error=./2.1_host_prediction/10_rafah/rafah.slurm.%j.err
+> #SBATCH --output=10_rafah/rafah.slurm.%j.out
+> #SBATCH --error=10_rafah/rafah.slurm.%j.err
+> 
+> assembly='../1.3_virus_identification/30_filter_contigs/assembly.fasta'
+> contigs='10_rafah/split_contigs'
+> mkdir -p "$contigs"
 > 
-> assembly='./1.3_virus_identification/40_results_filter_contigs/assembly.fasta'
-> contigs='./2.1_host_prediction/10_rafah/split_contigs'
->
 > # RaFAH expects each genome in a separate file. Activate our virtual environment
 > # and run a python script to split our filtered assembly into single files
-> source ./py3env/bin/activate
+> source ../py3env/bin/activate
 > 
 > # The script requires the assmbly path and a directory for outputting the contigs
-> python ./python_scripts/host_prediction/10_split_assembly_file.py $assembly $contigs
->
+> python ../python_scripts/2.1_split_assembly.py $assembly $contigs
+> 
 > # deactivate the python environment, just to be sure not to cause problems with the conda environment RaFAH needs
 > deactivate
->
+> 
 > # activate the conda environment with the dependencies RaFAH requires
 > source /vast/groups/VEO/tools/miniconda3_2024/etc/profile.d/conda.sh && conda activate perl_v5.32.1
->
+> 
 > # set a variable to call the RaFAH script
 > rafah='/home/groups/VEO/tools/rafah/RaFAH.pl'
 > 
@@ -255,21 +256,21 @@ Finally, we will combine the results from RaFAH and BLAST to compare the two met
 > # --extension: the extension of the contig files
 > # --file_prefix: can specify an output dir here and "run name" (rafah_1) here
 > 
-> perl "$rafah" --predict --genomes_dir $contigs --extension .fasta --file_prefix ./2.1_host_prediction/10_rafah/rafah_1
+> perl "$rafah" --predict --genomes_dir $contigs --extension .fasta --file_prefix 10_rafah/rafah_1
 > 
 > # deactivate RaFAH's conda environment
 > conda deactivate
->
+> 
 > # Our python script for translating the Taxonomy needs our python environment again
-> source ./py3env/bin/activate
->
+> source ../py3env/bin/activate
+> 
 > # set the path to the table with the translation between NCBI and GTDB and to RaFAH output
-> translation='./2.1_host_prediction/10_rafah/ncbi_to_gtdb.csv'
-> rafahtable='./2.1_host_prediction/10_rafah/rafah_1_Host_Predictions.tsv'
->
+> translation='10_rafah/ncbi_to_gtdb.csv'
+> rafahtable='10_rafah/rafah_1_Host_Predictions.tsv'
+> 
 > # run our script with the appropriate file names as parameters
-> python3 ./python_scripts/host_prediction/20_translate_taxonomy.py $rafahtable $translation ./2.1_host_prediction/10_rafah/rafah_1_Host_Predictions_gtdb.csv
->
+> python3 ../python_scripts/2.1_translate_ncbi_to_gtdb.py $rafahtable $translation 10_rafah/rafah_1_Host_Predictions_gtdb.csv
+> 
 > deactivate
 >```
 > {: .source}