diff --git a/02-run_programs/src/run_Wn.py b/02-run_programs/src/run_Wn.py index 0c2c57d5fdeed687892bdbcc524f43d4ff7160a5..f8d238bd40652902ef5ebe0b545303128d59bc7a 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 e1517a4ca55f25fdd389e263723feba3c43038b2..77af5796046c981cb3d46b097807e37cf4c146d0 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/)",