From 1fd3615c2cb4e8a1e56d37ed896bf09b351a2de8 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 9 Feb 2024 15:35:28 +0100
Subject: [PATCH] add predicthaplo

---
 .../predicthaplo_local_haplo.py               | 77 +++++++++++--------
 1 file changed, 44 insertions(+), 33 deletions(-)

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
index db9a0bcf..5e7293eb 100644
--- a/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo_local_haplo.py
+++ b/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo_local_haplo.py
@@ -2,11 +2,24 @@
 # CONDA: cxx-compiler = 1.4.1
 # CONDA: make = 4.3
 # CONDA: cmake = 3.22.1
+# CONDA: rhash = 1.4.4
 # CONDA: liblapack = 3.9.0
 # CONDA: gtest = 1.11.0
 # CONDA: samtools = 1.15.1
 # CONDA: biopython = 1.79
 
+"""
+To execute PredictHaplo on Euler, I have to load the following:
+source /cluster/apps/local/env2lmod.sh # scp doesn't know env2lmod
+export MY_MODULEPATH_ROOT=/cluster/work/bewi/nss/modules/
+module use $MY_MODULEPATH_ROOT/Core
+module load  gcc/5.4.0 openblas/0.2.19
+. /cluster/work/bewi/members/lfuhrmann/miniconda3/bin/activate
+cd /cluster/work/bewi/members/lfuhrmann/
+conda activate snakemake
+"""
+
+
 import subprocess
 from pathlib import Path
 
@@ -15,6 +28,23 @@
 from Bio.SeqRecord import SeqRecord
 
 
+def write_config_file(fname_ref, fname_sam,fname_config, ph_prefix):
+    with open('original_file.txt', 'r') as file:
+        content = file.readlines()
+
+    modified_content =  content
+    modified_content[2] = str(ph_prefix)
+    modified_content[4] = str(fname_ref)
+    modified_content[6] = "0"
+    modified_content[8] = str(fname_sam)
+    modified_content[10] = "0"
+    modified_content[12] = str(fname_ref)
+    modified_content[16] = "10000"
+
+    with open(fname_config, 'w') as file:
+        file.writelines(modified_content)
+
+
 def main(fname_bam,
          fname_reference,
          fname_results_snv,
@@ -25,52 +55,33 @@ def main(fname_bam,
 ):
     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,
-    )
+    predicthaplo_exe = "/cluster/work/bewi/members/lfuhrmann/PredictHaplo-1.1/PredictHaplo"
 
-    repo_dir = dname_work / "PredictHaplo"
+    # prepare environment
     subprocess.run(
-        ["cmake", "-DCMAKE_BUILD_TYPE=Release", "-B", "build", "-S", "."],
-        cwd=repo_dir,
+        ["samtools", "view", "-h", "-o", dname_work / "reads.sam", fname_bam],
         check=True,
     )
-    subprocess.run(["cmake", "--build", "build"], cwd=repo_dir, check=True)
 
-    exec_path = repo_dir / "build" / "predicthaplo"
+    fname_sam = (dname_work / "reads.sam").resolve()
 
-    # prepare environment
+    # copy example config file
     subprocess.run(
-        ["samtools", "view", "-h", "-o", dname_work / "reads.sam", fname_bam],
+        ["wget", "https://github.com/bmda-unibas/PredictHaplo/blob/master/config_5V"],
+        cwd=dname_work,
         check=True,
     )
 
+    # modify config file for predicthaplo
+    fname_config = (dname_work / "predicthaplo_config").resolve()
+    ph_prefix = (dname_work / "predicthaplo_output").resolve()
+    write_config_file(Path(fname_reference).resolve(), fname_sam, fname_config, ph_prefix)
+
     # 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",
+            predicthaplo_exe,
+            str(fname_config),
         ],
         check=True,
     )