Create bioinformatics_testing.py

notebooks/GenAI/example_scripts/bioinformatics_testing.py

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+import pandas as pd
+import subprocess
+
+# Step 1: Read the sample sheet
+sample_sheet = pd.read_csv('samplesheet.csv')
+
+# Step 2: Run FastQC
+for index, row in sample_sheet.iterrows():
+    fastqc_command = f"fastqc {row['file_path']} -o ./fastqc_results/"
+    subprocess.run(fastqc_command, shell=True)
+
+# Step 3: Run MultiQC
+multiqc_command = "multiqc ./fastqc_results/ -o ./multiqc_report/"
+subprocess.run(multiqc_command, shell=True)
+
+# Step 4: Run STAR aligner
+for index, row in sample_sheet.iterrows():
+    star_command = f"STAR --genomeDir /path/to/genome --readFilesIn {row['file_path']} --outFileNamePrefix ./star_results/{row['sample_id']}"
+    subprocess.run(star_command, shell=True)
+
+# Step 5: Index BAM files with Samtools
+for index, row in sample_sheet.iterrows():
+    bam_file = f"./star_results/{row['sample_id']}.bam"
+    samtools_command = f"samtools index {bam_file}"
+    subprocess.run(samtools_command, shell=True) 
+