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Adding gc-percentage calculation and reporting to stdout #9

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Adding gc-percentage calculation and reporting to stdout #9

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dbd4f38
adding gc-percentage calculation and reporting
DOH-HNH0303 Jul 10, 2024
f4f64e7
Update fastq-peek.sh to fit style guide
DOH-HNH0303 Jul 10, 2024
d983f00
Update test.yml to incl GC_PERCENT test
DOH-HNH0303 Jul 10, 2024
c0c8e0a
fix typo in test.yml
DOH-HNH0303 Jul 10, 2024
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1 change: 1 addition & 0 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ 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 Percent in ./data/sample.fastq: 0.5" >> 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
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14 changes: 13 additions & 1 deletion bin/fastq-peek.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
#!/bin/bash

# Holly Halstead
# Western-WFD-2024 Week 01 Exercise

# Get the directory of the current script
SCRIPT_DIR=$(dirname "$0")

Expand All @@ -24,5 +27,14 @@ echo "Processing FASTQ file: $FASTQ_FILE"
LINE_COUNT=$(wc -l < "$FASTQ_FILE")
## Calculate the number of reads (4 lines per read)
READ_COUNT=$((LINE_COUNT / 4))
## Count GC in FASTQ file
GC_COUNT=$(awk '(NR%4==2) {gsub(/[ATnNat]/,"");N+=length($0);}END{print N;}' "$FASTQ_FILE")
## Count total number of bases in FASTQ file
TOTAL_BASE_COUNT=$(awk 'NR%4==2 {sum += length($0)} END {print sum}' "$FASTQ_FILE")
## Calculate GC percent in FASTQ file
GC_PERCENT=$(awk '(NR%4==2) {N1+=length($0);gsub(/[AT]/,"");N2+=length($0);}END{print N2/N1;}' "$FASTQ_FILE")

# Print results to terminal
echo -e "Number of reads in $FASTQ_FILE: $READ_COUNT\nGC Percent in $FASTQ_FILE: $GC_PERCENT"

echo "Number of reads in $FASTQ_FILE: $READ_COUNT"
exit 0
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