From b0a826ce19c62a8106b32bb946208b668ac89f3b Mon Sep 17 00:00:00 2001 From: Tatiana Gurbich Date: Tue, 19 Nov 2024 13:29:59 +0000 Subject: [PATCH] Replaced dashes with underscores in database_import_scripts --- .../rnacentral/calculate_model_lengths.py | 0 .../rnacentral/generate_rnacentral_json.py | 0 .../rnacentral/rfam_model_lengths.txt | 0 .../rnacentral/rfam_model_lengths_14.9.txt | 0 .../uniprot/__init__.py | 0 .../uniprot/convert_gbk.py | 0 .../uniprot/generate_uniprot_metadata.py | 0 .../uniprot/gtdb_to_ncbi_majority_vote.py | 0 .../uniprot/gtdb_to_ncbi_majority_vote_v2.py | 0 .../uniprot/preprocess_taxonomy_for_uniprot.py | 0 .../uniprot/uniprot_sanity_check.py | 0 helpers/file_organiser.sh | 6 +++--- tests/scripts/test_generate_rnacentral_json.py | 4 ++-- 13 files changed, 5 insertions(+), 5 deletions(-) rename helpers/{database-import-scripts => database_import_scripts}/rnacentral/calculate_model_lengths.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/rnacentral/generate_rnacentral_json.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/rnacentral/rfam_model_lengths.txt (100%) rename helpers/{database-import-scripts => database_import_scripts}/rnacentral/rfam_model_lengths_14.9.txt (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/__init__.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/convert_gbk.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/generate_uniprot_metadata.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/gtdb_to_ncbi_majority_vote.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/gtdb_to_ncbi_majority_vote_v2.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/preprocess_taxonomy_for_uniprot.py (100%) rename helpers/{database-import-scripts => database_import_scripts}/uniprot/uniprot_sanity_check.py (100%) diff --git a/helpers/database-import-scripts/rnacentral/calculate_model_lengths.py b/helpers/database_import_scripts/rnacentral/calculate_model_lengths.py similarity index 100% rename from helpers/database-import-scripts/rnacentral/calculate_model_lengths.py rename to helpers/database_import_scripts/rnacentral/calculate_model_lengths.py diff --git a/helpers/database-import-scripts/rnacentral/generate_rnacentral_json.py b/helpers/database_import_scripts/rnacentral/generate_rnacentral_json.py similarity index 100% rename from helpers/database-import-scripts/rnacentral/generate_rnacentral_json.py rename to helpers/database_import_scripts/rnacentral/generate_rnacentral_json.py diff --git a/helpers/database-import-scripts/rnacentral/rfam_model_lengths.txt b/helpers/database_import_scripts/rnacentral/rfam_model_lengths.txt similarity index 100% rename from helpers/database-import-scripts/rnacentral/rfam_model_lengths.txt rename to helpers/database_import_scripts/rnacentral/rfam_model_lengths.txt diff --git a/helpers/database-import-scripts/rnacentral/rfam_model_lengths_14.9.txt b/helpers/database_import_scripts/rnacentral/rfam_model_lengths_14.9.txt similarity index 100% rename from helpers/database-import-scripts/rnacentral/rfam_model_lengths_14.9.txt rename to helpers/database_import_scripts/rnacentral/rfam_model_lengths_14.9.txt diff --git a/helpers/database-import-scripts/uniprot/__init__.py b/helpers/database_import_scripts/uniprot/__init__.py similarity index 100% rename from helpers/database-import-scripts/uniprot/__init__.py rename to helpers/database_import_scripts/uniprot/__init__.py diff --git a/helpers/database-import-scripts/uniprot/convert_gbk.py b/helpers/database_import_scripts/uniprot/convert_gbk.py similarity index 100% rename from helpers/database-import-scripts/uniprot/convert_gbk.py rename to helpers/database_import_scripts/uniprot/convert_gbk.py diff --git a/helpers/database-import-scripts/uniprot/generate_uniprot_metadata.py b/helpers/database_import_scripts/uniprot/generate_uniprot_metadata.py similarity index 100% rename from helpers/database-import-scripts/uniprot/generate_uniprot_metadata.py rename to helpers/database_import_scripts/uniprot/generate_uniprot_metadata.py diff --git a/helpers/database-import-scripts/uniprot/gtdb_to_ncbi_majority_vote.py b/helpers/database_import_scripts/uniprot/gtdb_to_ncbi_majority_vote.py similarity index 100% rename from helpers/database-import-scripts/uniprot/gtdb_to_ncbi_majority_vote.py rename to helpers/database_import_scripts/uniprot/gtdb_to_ncbi_majority_vote.py diff --git a/helpers/database-import-scripts/uniprot/gtdb_to_ncbi_majority_vote_v2.py b/helpers/database_import_scripts/uniprot/gtdb_to_ncbi_majority_vote_v2.py similarity index 100% rename from helpers/database-import-scripts/uniprot/gtdb_to_ncbi_majority_vote_v2.py rename to helpers/database_import_scripts/uniprot/gtdb_to_ncbi_majority_vote_v2.py diff --git a/helpers/database-import-scripts/uniprot/preprocess_taxonomy_for_uniprot.py b/helpers/database_import_scripts/uniprot/preprocess_taxonomy_for_uniprot.py similarity index 100% rename from helpers/database-import-scripts/uniprot/preprocess_taxonomy_for_uniprot.py rename to helpers/database_import_scripts/uniprot/preprocess_taxonomy_for_uniprot.py diff --git a/helpers/database-import-scripts/uniprot/uniprot_sanity_check.py b/helpers/database_import_scripts/uniprot/uniprot_sanity_check.py similarity index 100% rename from helpers/database-import-scripts/uniprot/uniprot_sanity_check.py rename to helpers/database_import_scripts/uniprot/uniprot_sanity_check.py diff --git a/helpers/file_organiser.sh b/helpers/file_organiser.sh index 3362765b..8a0db9df 100755 --- a/helpers/file_organiser.sh +++ b/helpers/file_organiser.sh @@ -51,8 +51,8 @@ function GenerateRNACentralJSON { echo "Running JSON generation" mitload miniconda && conda activate pybase - rna_cmd="python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database-import-scripts/rnacentral/generate_rnacentral_json.py \ - -r /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database-import-scripts/rnacentral/rfam_model_lengths_14.9.txt \ + rna_cmd="python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database_import_scripts/rnacentral/generate_rnacentral_json.py \ + -r /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database_import_scripts/rnacentral/rfam_model_lengths_14.9.txt \ -m "${RESULTS_PATH}/genomes-all_metadata.tsv" -o "${RESULTS_PATH}/additional_data/rnacentral/${CATALOGUE_FOLDER}-rnacentral.json" \ -d "${RESULTS_PATH}/additional_data/ncrna_deoverlapped_species_reps/" -g "${RESULTS_PATH}/additional_data/rnacentral/GFFs/ "\ -f "${RESULTS_PATH}/additional_data/mgyg_genomes/"" @@ -134,7 +134,7 @@ function GenerateUniprotFiles { fi mitload miniconda && conda activate pybase - python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database-import-scripts/uniprot/preprocess_taxonomy_for_uniprot.py \ + python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database_import_scripts/uniprot/preprocess_taxonomy_for_uniprot.py \ -g ${RESULTS_PATH}/additional_data/gtdbtk_results/ -r "r214" -v "2" \ -m ${RESULTS_PATH}/ftp/genomes-all_metadata.tsv --species-level-taxonomy -t 4 \ -o ${RESULTS_PATH}/additional_data/uniprot/preprocessed_taxonomy.tsv diff --git a/tests/scripts/test_generate_rnacentral_json.py b/tests/scripts/test_generate_rnacentral_json.py index 0beb5f56..def7402c 100644 --- a/tests/scripts/test_generate_rnacentral_json.py +++ b/tests/scripts/test_generate_rnacentral_json.py @@ -6,10 +6,10 @@ from pathlib import Path script_dir = Path(__file__).resolve().parent -rnacentral_dir = script_dir / '../../helpers/database-import-scripts/rnacentral' +rnacentral_dir = script_dir / '../../helpers/database_import_scripts/rnacentral' rnacentral_dir = rnacentral_dir.resolve() -generate_json = importlib.import_module("helpers.database-import-scripts.rnacentral.generate_rnacentral_json") +generate_json = importlib.import_module("helpers.database_import_scripts.rnacentral.generate_rnacentral_json") generate_metadata_dict = generate_json.generate_metadata_dict get_good_hits = generate_json.get_good_hits load_rfam = generate_json.load_rfam