From 85fa7844525557c3be8cf062610cc89ec960ab31 Mon Sep 17 00:00:00 2001 From: valentynbez Date: Mon, 10 Jun 2024 16:45:47 +0200 Subject: [PATCH] fix: update module names --- mDeepFRI/bio_utils.py | 2 +- mDeepFRI/cli.py | 25 ++++++++++++++++++++++--- 2 files changed, 23 insertions(+), 4 deletions(-) diff --git a/mDeepFRI/bio_utils.py b/mDeepFRI/bio_utils.py index cb5d609..6cb3de5 100644 --- a/mDeepFRI/bio_utils.py +++ b/mDeepFRI/bio_utils.py @@ -11,7 +11,7 @@ from biotite.structure.io.pdbx import PDBxFile, get_structure from mDeepFRI.alignment import AlignmentResult -from mDeepFRI.alignment_utils import align_contact_map, pairwise_sqeuclidean +from mDeepFRI.contact_map_utils import align_contact_map, pairwise_sqeuclidean logger = logging.getLogger(__name__) handler = logging.StreamHandler(sys.stdout) diff --git a/mDeepFRI/cli.py b/mDeepFRI/cli.py index 9c34dce..1a34855 100644 --- a/mDeepFRI/cli.py +++ b/mDeepFRI/cli.py @@ -95,6 +95,7 @@ def get_models(output, version): "--db-path", required=True, type=click.Path(exists=True), + multiple=True, help="Path to a structures database compessed with FoldComp.", ) @click.option( @@ -179,9 +180,9 @@ def get_models(output, version): is_flag=True, help="Skip PDB100 database search.", ) -def search_databases(input, output, db_path, min_length, max_length, min_bits, - max_eval, min_ident, min_coverage, top_k, overwrite, - threads, skip_pdb): +def search_databases(input, output, db_path, sensitivity, min_length, + max_length, min_bits, max_eval, min_ident, min_coverage, + top_k, overwrite, threads, skip_pdb): """ Hierarchically search FoldComp databases for similar proteins with MMSeqs2. Based on the thresholds from https://doi.org/10.1038/s41586-023-06510-w. @@ -204,9 +205,27 @@ def search_databases(input, output, db_path, min_length, max_length, min_bits, # "skip_pdb": skip_pdb # } + # write command parameters to log + logger.info("Command parameters:") + logger.info("Input: %s", input) + logger.info("Output: %s", output) + logger.info("Database: %s", db_path) + logger.info("Sensitivity: %s", sensitivity) + logger.info("Minimum length: %s", min_length) + logger.info("Maximum length: %s", max_length) + logger.info("Minimum bitscore: %s", min_bits) + logger.info("Maximum e-value: %s", max_eval) + logger.info("Minimum identity: %s", min_ident) + logger.info("Minimum coverage: %s", min_coverage) + logger.info("Top k results: %s", top_k) + logger.info("Overwrite: %s", overwrite) + logger.info("Threads: %s", threads) + logger.info("Skip PDB: %s", skip_pdb) + hierarchical_database_search(query_file=input, databases=db_path, output_path=output, + sensitivity=sensitivity, min_seq_len=min_length, max_seq_len=max_length, min_bits=min_bits,