From dc00fe02953d28c8c576b0a646b2f3b5da465afa Mon Sep 17 00:00:00 2001
From: Swastik Mishra <swastik.mishra@hhu.de>
Date: Wed, 28 May 2025 08:24:01 +0000
Subject: [PATCH] correct default paths
---
02-run_programs/src/run_Wn.py | 8 ++++----
02-run_programs/src/run_rangerdtl.py | 8 ++++----
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/02-run_programs/src/run_Wn.py b/02-run_programs/src/run_Wn.py
index 0c2c57d..f8d238b 100644
--- a/02-run_programs/src/run_Wn.py
+++ b/02-run_programs/src/run_Wn.py
@@ -407,10 +407,10 @@ def calculate_genome_Typicality(genome_path, gene_positions, template_size, tmp_
if __name__ == '__main__':
# parse arguments
parser = argparse.ArgumentParser()
- parser.add_argument("--gene-positions", "-g", type=str, required=False, default="/root/work/projects/hgt_inference_comparative_study/data/1236_gene_features.tsv",
- help="(str) Path to gene positions TSV file, with column headers: locus_tag, gene_id, start, end, strand, seqid, genome_accession, taxon_id. Default: /root/work/projects/hgt_inference_comparative_study/data/1236_gene_features.tsv")
- parser.add_argument("--genome-paths", "-p", type=str, required=False, default="/root/work/projects/hgt_inference_comparative_study/data/1236_genome_fna_filepaths.tsv",
- help="(str) Path to genome paths TSV file, with columns: genome_accession, genome_path. Default: /root/work/projects/hgt_inference_comparative_study/data/1236_genome_fna_filepaths.tsv")
+ parser.add_argument("--gene-positions", "-g", type=str, required=False, default="/root/work/projects/paper_comparative_study_of_hgt_inference_methods/data/1236_gene_features.tsv",
+ help="(str) Path to gene positions TSV file, with column headers: locus_tag, gene_id, start, end, strand, seqid, genome_accession, taxon_id. Default: /root/work/projects/paper_comparative_study_of_hgt_inference_methods/data/1236_gene_features.tsv")
+ parser.add_argument("--genome-paths", "-p", type=str, required=False, default="/root/work/projects/paper_comparative_study_of_hgt_inference_methods/data/1236_genome_fna_filepaths.tsv",
+ help="(str) Path to genome paths TSV file, with columns: genome_accession, genome_path. Default: /root/work/projects/paper_comparative_study_of_hgt_inference_methods/data/1236_genome_fna_filepaths.tsv")
parser.add_argument("--output-dir", "-o", type=str, required=False, default="Results/",
help="(str) Path to output directory. Default: Results/")
parser.add_argument("--threads", "-t", type=int, default=100,
diff --git a/02-run_programs/src/run_rangerdtl.py b/02-run_programs/src/run_rangerdtl.py
index e1517a4..77af579 100644
--- a/02-run_programs/src/run_rangerdtl.py
+++ b/02-run_programs/src/run_rangerdtl.py
@@ -87,10 +87,10 @@ if __name__ == '__main__':
# import argparse and read in the arguments
import argparse
parser = argparse.ArgumentParser()
- parser.add_argument("--speciestree", "-s", help="Path to the species tree (default: ../../data/1236_wol_tree_pruned_with_internal_labels.nwk)",
- type=str, default="../../data/1236_wol_tree_pruned_with_internal_labels.nwk")
- parser.add_argument("--genetrees", "-g", help="Path to the gene trees (default: ../../data/1236_pruned_gene_trees.tsv.rooted.underscored)", type=str,
- default="../../data/1236_pruned_gene_trees.tsv.rooted.underscored")
+ parser.add_argument("--speciestree", "-s", help="Path to the species tree (default: ../../1236_wol_tree_pruned_with_internal_labels.nwk)",
+ type=str, default="../../1236_wol_tree_pruned_with_internal_labels.nwk")
+ parser.add_argument("--genetrees", "-g", help="Path to the gene trees (default: ../../1236_pruned_gene_trees.tsv.rooted.underscored)", type=str,
+ default="../../1236_pruned_gene_trees.tsv.rooted.underscored")
parser.add_argument("--threads", "-t",
help="Number of threads to use (default: 50)", type=int, default=50)
parser.add_argument("--bin", "-b", help="Path to the Ranger bin directory (default: /root/bin/RANGERDTL_LINUX/)",
--
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