correct default paths

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,

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/)",