Group3

01_GitHub/scripts/03-annotation.sh

@@ -14,25 +14,17 @@ echo "Running annotation against database of glucocorticoid-responsive genes"
 
 for FILE in "$READS_DIR"/*.fastq.gz; 
 do 
-
     echo "Annotating file: $FILE"
-
-    # GROUP 3 - WRITE HERE THE COMMAND TO RUN DIAMOND BLASTX
-    # READS ARE GZIPPED AT $READS_DIR
-    # OUTPUT SHOULD GO TO $RESULTS_DIR, WITH FILENAME FORMAT: sample_matches.tab
-    # USE $DB AS THE DIAMOND DATABASE, $THREADS FOR THREADS, AND $MAX_TARGET_SEQS FOR MAX TARGET SEQS
-    # OUTFMT SHOULD BE 6 (TABULAR)
-    # tips below
-
 
+    diamond blastx -d "$DB" -q "$FILE" -o "$RESULTS_DIR"/$(basename "$FILE" .fastq.gz)_matches.tab --threads "$THREADS" --max-target-seqs "$MAX_TARGET_SEQS" --outfmt 6
 done
 
+
+
 # check if 12 annotation results were generated, and exit code 1 if not
 if [ $(ls "$RESULTS_DIR"/*_matches.tab | wc -l) -ne $N_FILES ]; then
     echo "Error: Not all annotation results were generated. Expected $N_FILES, but found $(ls "$RESULTS_DIR"/*_matches.tab | wc -l)."
     exit 1
 fi
 
-# tip: $(basename "$FILE" .fastq.gz) extracts the sample name from the filename by removing the directory path and the .fastq.gz extension
-
 echo "Annotation complete"