From 654897c29e8955964aa709a8b4a302087c847131 Mon Sep 17 00:00:00 2001
From: Swastik Mishra <swastik.mishra@hhu.de>
Date: Wed, 28 May 2025 08:23:35 +0000
Subject: [PATCH] correct paths and add error handling for py2 requirement
---
02-run_programs/src/run_angst.py | 27 +++++++++++++++++++++++----
1 file changed, 23 insertions(+), 4 deletions(-)
diff --git a/02-run_programs/src/run_angst.py b/02-run_programs/src/run_angst.py
index a212e64..b0dddc8 100644
--- a/02-run_programs/src/run_angst.py
+++ b/02-run_programs/src/run_angst.py
@@ -7,6 +7,7 @@ import logging
import shutil
from datetime import timedelta
from ete3 import Tree
+import traceback
# Create or get the logger
logger = logging.getLogger(__name__)
@@ -56,11 +57,29 @@ def run_ANGST_on_NOG(pool_args):
# Run AnGST
try:
logger.info("Running AnGST for NOG_ID {}".format(nog_id))
+ logger.info("Command: python2 {} {}".format(
+ angst_script, input_path))
+ # make sure python2 is available
+ py2_available = False
+ for path in os.environ["PATH"].split(os.pathsep):
+ full_path = os.path.join(path, "python2")
+ if os.path.isfile(full_path) and os.access(full_path, os.X_OK):
+ py2_available = True
+ break
+ if not py2_available:
+ logger.error("python2 is not available in PATH")
+ raise EnvironmentError("python2 is not available in PATH. Make sure you are in the correct conda environment.")
+
subprocess.check_call(["python2", angst_script, input_path])
except subprocess.CalledProcessError as e:
logger.error(
"AnGST failed for NOG_ID {} with error\n {}".format(nog_id, e))
return None
+ except Exception as e:
+ logger.error(
+ "AnGST failed for NOG_ID {} with error\n {}".format(nog_id, e))
+ logger.error(traceback.format_exc())
+ return None
return nog_id
@@ -93,10 +112,10 @@ if __name__ == '__main__':
# use argparse for reading in the number of threads and the input trees file
parser = argparse.ArgumentParser(
description="Run AnGST on a set of gene trees")
- parser.add_argument("--species", "-s", type=str, default="../../data/1236_wol_tree_pruned_angst.nwk",
- help="Path to species tree file (default: ../../data/1236_wol_tree_pruned_angst.nwk)")
- parser.add_argument("--gene", "-g", type=str, default="../../data/1236_pruned_gene_trees.tsv",
- help="Path to gene trees file (default: ../../data/1236_pruned_gene_trees.tsv)")
+ parser.add_argument("--species", "-s", type=str, default="../../1236_wol_tree_pruned_angst.nwk",
+ help="Path to species tree file (default: ../../1236_wol_tree_pruned_angst.nwk)")
+ parser.add_argument("--gene", "-g", type=str, default="../../1236_pruned_gene_trees.tsv",
+ help="Path to gene trees file (default: ../../1236_pruned_gene_trees.tsv)")
parser.add_argument("--threads", "-t", type=int, default=50,
help="Number of threads to use for parallelization (default: 50)")
parser.add_argument("--output", "-o", type=str, default="./Results",
--
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