From 503ff8b21fc0608ad7233f3e5f875b2b4c0ba7d7 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 3 Jan 2024 12:11:59 +0100
Subject: [PATCH] [local_haplo] add predicthaplo

---
 .../predicthaplo_local_haplo.py               | 110 ++++++++++++++++++
 1 file changed, 110 insertions(+)
 create mode 100644 resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo_local_haplo.py

diff --git a/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo_local_haplo.py b/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo_local_haplo.py
new file mode 100644
index 00000000..db9a0bcf
--- /dev/null
+++ b/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo_local_haplo.py
@@ -0,0 +1,110 @@
+# GROUP: global
+# CONDA: cxx-compiler = 1.4.1
+# CONDA: make = 4.3
+# CONDA: cmake = 3.22.1
+# CONDA: liblapack = 3.9.0
+# CONDA: gtest = 1.11.0
+# CONDA: samtools = 1.15.1
+# CONDA: biopython = 1.79
+
+import subprocess
+from pathlib import Path
+
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+def main(fname_bam,
+         fname_reference,
+         fname_results_snv,
+         fname_result_haplos,
+         dname_work,
+         seq_type,
+         threads,
+):
+    dname_work.mkdir(parents=True, exist_ok=True)
+
+    # compile tool
+    subprocess.run(
+        ["git", "clone", "https://github.com/cbg-ethz/PredictHaplo.git"],
+        cwd=dname_work,
+        check=True,
+    )
+
+    repo_dir = dname_work / "PredictHaplo"
+    subprocess.run(
+        ["cmake", "-DCMAKE_BUILD_TYPE=Release", "-B", "build", "-S", "."],
+        cwd=repo_dir,
+        check=True,
+    )
+    subprocess.run(["cmake", "--build", "build"], cwd=repo_dir, check=True)
+
+    exec_path = repo_dir / "build" / "predicthaplo"
+
+    # prepare environment
+    subprocess.run(
+        ["samtools", "view", "-h", "-o", dname_work / "reads.sam", fname_bam],
+        check=True,
+    )
+
+    # execute tool
+    ph_prefix = dname_work / "predicthaplo_output"
+    subprocess.run(
+        [
+            exec_path,
+            "--sam",
+            dname_work / "reads.sam",
+            "--reference",
+            fname_reference,
+            "--prefix",
+            ph_prefix,
+            "--reconstructed_haplotypes",
+            fname_result,
+            "--have_true_haplotypes",
+            "0",
+            "--min_align_score_fraction",
+            "-1",
+            "--min_overlap_factor",
+            "0.1",
+            "--entropy_threshold",
+            "1e-4",
+            "--min_length",
+            "1",
+        ],
+        check=True,
+    )
+
+    # clean output file
+    record_list = []
+    for record in SeqIO.parse(fname_result, "fasta"):
+        props = str(record.seq).split("EndOfComments")[0]
+        seq = str(record.seq).split("EndOfComments")[-1]
+
+        desc = props.split(";")[1]  # only keep frequency
+
+        rec = SeqRecord(
+            Seq(seq.replace("-", "")),
+            id=record.id,
+            description=desc,
+        )
+        record_list.append(rec)
+
+    SeqIO.write(record_list, fname_result, "fasta")
+
+    # create empty vcf files
+    f = open(fname_results_snv, "a")
+    f.write("#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO")
+    f.close()
+
+
+if __name__ == "__main__":
+    main(
+        Path(snakemake.input.fname_bam),
+        Path(snakemake.input.fname_reference),
+        Path(snakemake.output.fname_result),
+        Path(snakemake.output.fname_result_haplos),
+        Path(snakemake.output.dname_work),
+        snakemake.wildcards.seq_tech,
+        snakemake.threads,
+    )