Translated other Blastn scripts

scripts/blastn-array.sh

@@ -4,18 +4,17 @@
 #SBATCH --mem-per-cpu=2000M
 #SBATCH --time=0-00:20
 
-cd $SLURM_SUBMIT_DIR
 if [ "$(basename $PWD)" = "scripts" ]; then
   cd ..
 fi
-cd donnees
+cd data
 
 module load gcc/9.3.0 blast+/2.12.0 seqkit/0.15.0
 
-INCONNUS=(M N O P Q R)
-INC_X="${INCONNUS[$SLURM_ARRAY_TASK_ID]}"
+UNKNOWNS=(M N O P Q R)
+UNK_X="${UNKNOWNS[$SLURM_ARRAY_TASK_ID]}"
 mkdir -p res_array
 
-parallel blastn -db espece_{1} \
-  -query chr_$INC_X.fa.split/chr_$INC_X.part_0{2}.fa \
-  '>' res_array/align_${INC_X}_{1}_{2} ::: A B C D ::: {01..10}
+parallel blastn -db species_{1} \
+  -query chr_$UNK_X.fa.split/chr_$UNK_X.part_0{2}.fa \
+  '>' res_array/align_${UNK_X}_{1}_{2} ::: A B C D ::: {01..10}

scripts/blastn-glost.sh

@@ -3,7 +3,6 @@
 #SBATCH --mem-per-cpu=2000M
 #SBATCH --time=0-00:20
 
-cd $SLURM_SUBMIT_DIR
 if [ "$(basename $PWD)" = "scripts" ]; then
   cd ..
 fi

scripts/blastn-parallel.sh

@@ -3,15 +3,14 @@
 #SBATCH --mem-per-cpu=2000M
 #SBATCH --time=0-00:20
 
-cd $SLURM_SUBMIT_DIR
 if [ "$(basename $PWD)" = "scripts" ]; then
   cd ..
 fi
-cd donnees
+cd data
 
 module load gcc/9.3.0 blast+/2.12.0 seqkit/0.15.0
 
 mkdir -p res_prll
 
-parallel 'blastn -db espece_{1} -query chr_{2}.fa > res_prll/align_{2}_{1}' \
+parallel 'blastn -db species_{1} -query chr_{2}.fa > res_prll/align_{2}_{1}' \
   ::: A B C D ::: K L M N O P Q R S T U V W X Y Z

scripts/blastn-pipeline.sh

@@ -1,18 +1,18 @@
 #!/bin/bash
 
-echo '- Aller à la racine du matériel ...'
+echo '- Going to the root of the material ...'
 cd $(dirname $0)/..
 CIP201=$PWD
 
-echo '- Importer les données dans $SCRATCH ...'
-mkdir -p $SCRATCH/donnees
-rsync -a donnees/ $SCRATCH/donnees/
+echo '- Copying the data to $SCRATCH ...'
+mkdir -p $SCRATCH/data
+rsync -a data/ $SCRATCH/data/
 cd $SCRATCH
 
-echo '- Soumettre la première tâche ...'
-TACHE1=$(sbatch --parsable $CIP201/scripts/blastn-gen-seq.sh)
-echo '  - Numéro de tâche initiale :' $TACHE1
+echo '- Submitting the first job ...'
+JOB1=$(sbatch --parsable $CIP201/scripts/blastn-gen-seq.sh)
+echo '  - First job ID:' $JOB1
 
-echo '- Soumettre la tâche dépendante ...'
-sbatch --dependency=afterok:$TACHE1 $CIP201/scripts/blastn-parallel.sh
+echo '- Submitting the second job that depends on the first one ...'
+sbatch --dependency=afterok:$JOB1 $CIP201/scripts/blastn-parallel.sh
 squeue -u $USER

scripts/blastn-postprocess.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+RESULTS=$SCRATCH/data/res_prll
+MY_PROJECT=$(ls -d $HOME/projects/def-*/$USER)
+FINAL_TSV=$MY_PROJECT/results.tsv
+
+cd $RESULTS
+
+echo -e 'unknown\tspecies\tpercentage' > $FINAL_TSV
+
+for filename in $(ls); do
+  unknown=$(echo $filename | cut -d_ -f2)
+  species=$(echo $filename | cut -d_ -f3)
+  echo -en "$unknown\t$species\t"
+
+  grep Identities $filename | awk '{print $3}' | tr '/' ' ' | awk '
+    BEGIN {m=0; b=0;}
+    {m+=$1; b+=$2;}
+    END {b++; percent=100.0*m/b; print percent"%"}'
+done >> $FINAL_TSV
+
+echo $FINAL_TSV
+cat $FINAL_TSV