From f2edb2fc08a93036d589aab1b1000dd820705d36 Mon Sep 17 00:00:00 2001 From: RaulFD-creator Date: Mon, 20 Jan 2025 09:32:00 +0000 Subject: [PATCH] =?UTF-8?q?=F0=9F=AA=B2=20Bug-fix:=20Include=20the=20folds?= =?UTF-8?q?eek=20tmp=20in=20hestia=5Ftmp?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- hestia/similarity.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/hestia/similarity.py b/hestia/similarity.py index d6ae0de..0bd88a1 100644 --- a/hestia/similarity.py +++ b/hestia/similarity.py @@ -535,9 +535,10 @@ def protein_structure_similarity( if df_target is None: df_target = df_query tmp_dir = f'hestia_tmp_{time.time()}' + if os.path.isdir(tmp_dir): shutil.rmtree(tmp_dir) - os.mkdir(tmp_dir) + os.makedirs(tmp_dir) if verbose > 2: mmseqs_v = 3 else: @@ -575,7 +576,7 @@ def protein_structure_similarity( prefilter = '0' if prefilter else '2' subprocess.run([foldseek, 'search', db_query, db_target, alignment_db, - 'tmp', '-s', '9.5', '-a', '-e', 'inf', + f'{tmp_dir}/tmp', '-s', '9.5', '-a', '-e', 'inf', '--seq-id-mode', denominator, '--threads', str(threads), '--alignment-type', representation, '--prefilter-mode', prefilter, '-v', str(mmseqs_v) @@ -602,7 +603,8 @@ def protein_structure_similarity( else: df = df.rename({'prob': 'metric'}) df = df.with_columns(pl.col("metric").map_elements( - lambda x: qry2idx[x.split('.pdb')[0].split('_')[0]] + lambda x: qry2idx[x.split('.pdb')[0].split('_')[0]], + return_dtype=pl.Int64 )) df = df.with_columns(pl.col('query').map_elements( lambda x: qry2idx[x.split('.pdb')[0].split('_')[0]], @@ -618,7 +620,7 @@ def protein_structure_similarity( if filename is None: filename = time.time() df.write_csv(f'{filename}.csv.gz', compression='gzip') - + shutil.rmtree(tmp_dir) return df