convert snippy and snippy-core to py script

scripts/snippy_core.py

@@ -0,0 +1,74 @@
+import subprocess as sp
+import sys
+from pathlib import Path
+
+CPUS = 8
+
+# Run script like: `python script_name.py /path/to/reads/ /path/to/reference_genome.fa`
+# Will probably want to submit this to the cluster for real datasets
+# Use an sbatch script and include the above as the main script body
+if __name__ == "__main__":
+    # Gather reads
+    # For now, manually excluding mock/control samples
+    reads_fp = Path(sys.argv[1])
+    reads_files = list(reads_fp.glob("*.fastq.gz"))
+    # Pair reads
+    samples = {
+        f.name.split("_1.fastq.gz")[0].split("_2.fastq.gz")[0] for f in reads_files
+    }
+    paired_reads = [
+        (sample, reads_fp / f"{sample}_1.fastq.gz", reads_fp / f"{sample}_2.fastq.gz")
+        for sample in samples
+    ]
+
+    # Select reference genome
+    # Again, for now, doing this manually
+    ref_fp = Path(sys.argv[2])
+
+    # Run snippy per-sample
+    for sample, r1, r2 in paired_reads:
+        outdir = Path("snippy_outputs") / sample
+        outdir.mkdir(parents=True, exist_ok=True)
+        cmd = [
+            "snippy",
+            "--cpus",
+            str(CPUS),
+            "--outdir",
+            str(outdir),
+            "--ref",
+            ref_fp,
+            "--R1",
+            str(r1),
+            "--R2",
+            str(r2),
+        ]
+        print("Running ", " ".join(cmd))
+        sp.run(cmd)
+
+    # Run snippy-core to create core SNP alignment
+    snippy_outdirs = [str(p) for p in Path("snippy_outputs").iterdir() if p.is_dir()]
+    core_outdir = Path("snippy_core_output")
+    core_outdir.mkdir(parents=True, exist_ok=True)
+    cmd = ["snippy-core", "--prefix", "core", *snippy_outdirs, "--ref", ref_fp]
+    print("Running ", " ".join(cmd))
+    sp.run(cmd, cwd=str(core_outdir), shell=True)
+
+    # Run iqtree on core SNP alignment
+    core_snp_alignment = core_outdir / "core.full.aln"
+    iqtree_outdir = core_outdir / "iqtree" / "core.full.aln.treefile"
+    iqtree_outdir.mkdir(parents=True, exist_ok=True)
+    cmd = [
+        "iqtree",
+        "-s",
+        str(core_snp_alignment),
+        "-m",
+        "MFP",
+        "-B",
+        "1000",
+        "-T",
+        "AUTO",
+        "-pre",
+        str(core_outdir),
+    ]
+    print("Running ", " ".join(cmd))
+    sp.run(cmd)