Merge pull request #11 from theiagen/jwe-gc-count-dev

Adding GC content calculations

.github/workflows/test.yml

@@ -25,7 +25,8 @@ jobs:  # Define jobs for the workflow
           # Save the expected output to a file
           echo "Processing FASTQ file: ./data/sample.fastq" > expected_output.txt
           echo "Number of reads in ./data/sample.fastq: 2" >> expected_output.txt
-
+          echo "GC Content of reads in ./data/sample.fastq: 50%" >> expected_output.txt
+          
           # Capture the actual output of the script and save it to a file
           ./bin/fastq-peek.sh ./data/sample.fastq > actual_output.txt
 

bin/fastq-peek.sh

@@ -25,4 +25,14 @@ LINE_COUNT=$(wc -l < "$FASTQ_FILE")
 ## Calculate the number of reads (4 lines per read)
 READ_COUNT=$((LINE_COUNT / 4))
 
+##Count A, C, T, and G nucleotides in reads
+TOTAL_BASE_COUNT=$(grep -o "A\|C\|T\|G" $FASTQ_FILE | wc -l)
+
+##Count G and C nucleotides in reads
+GC_COUNT=$(grep -o "G\|C" $FASTQ_FILE | wc -l)
+
+##Calculate GC Content of reads (X100 for % of total nts)
+GC_CONTENT=$(($GC_COUNT*100/$TOTAL_BASE_COUNT))
+
 echo "Number of reads in $FASTQ_FILE: $READ_COUNT"
+echo "GC Content of reads in $FASTQ_FILE: $GC_CONTENT%"