From 64a583f18d02607aadadfc4003b8aeb214a21968 Mon Sep 17 00:00:00 2001 From: RaulFD-creator Date: Mon, 11 Nov 2024 12:57:21 +0000 Subject: [PATCH 1/3] =?UTF-8?q?=F0=9F=9A=80=20Versions:=20Version=200.0.33?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 95346a1..04f88b8 100644 --- a/setup.py +++ b/setup.py @@ -48,6 +48,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/IBM/Hestia-OOD', - version='0.0.32', + version='0.0.33', zip_safe=False, ) From ae63d9f83cfea001963fbd374c503a309ff0e2c5 Mon Sep 17 00:00:00 2001 From: RaulFD-creator Date: Mon, 11 Nov 2024 12:58:24 +0000 Subject: [PATCH 2/3] =?UTF-8?q?=F0=9F=AA=B2=20Bug=20fix:=20`peptides`=20si?= =?UTF-8?q?milarity=20support=20for=20`None`=20`df=5Ftarget`?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- hestia/similarity.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/hestia/similarity.py b/hestia/similarity.py index 5ea9f22..85caf96 100644 --- a/hestia/similarity.py +++ b/hestia/similarity.py @@ -705,6 +705,8 @@ def _medium_alignment(df_query, df_target, tmp_dir, os.mkdir(tmp_dir) df_query['seq_len'] = df_query[field_name].map(len) + if df_target is None: + df_target = df_query normal_df_query = df_query[df_query['seq_len'] > 20] medium_df_query = df_query[(df_query['seq_len'] > 8) & (df_query['seq_len'] <= 20)] From c12a6c8e19c7cb56d165ed5e7b34cc72926dbb1c Mon Sep 17 00:00:00 2001 From: RaulFD-creator Date: Mon, 11 Nov 2024 13:05:14 +0000 Subject: [PATCH 3/3] =?UTF-8?q?=F0=9F=AA=B2=20Bug=20fix:=20`peptides`=20si?= =?UTF-8?q?milarity=20support=20for=20`None`=20`df=5Ftarget`?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- hestia/similarity.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/hestia/similarity.py b/hestia/similarity.py index 85caf96..c28c6e3 100644 --- a/hestia/similarity.py +++ b/hestia/similarity.py @@ -680,11 +680,12 @@ def _medium_alignment(df_query, df_target, tmp_dir, dbtype, db_target_file, '-v', '1', f'{tmp_dir}/db_target']) - subprocess.run(['mmseqs', 'search', f'{tmp_dir}/db_query', + subprocess.run(['mmseqs', 'search', f'{tmp_dir}/db_query', f'{tmp_dir}/db_target', f'{tmp_dir}/align_db', f'{tmp_dir}/tmp', '--alignment-mode', '3', '--seq-id-mode', denominator, '--search-type', '1', - '--prefilter-mode', '2', '-s', '2', '-v', mmseqs_v, + '--prefilter-mode', '2', '-s', '2', + '-v', str(mmseqs_v), '--threads', str(threads), '--mask', '0', '--comp-bias-corr', '0', '-e', '1e7']) @@ -741,7 +742,8 @@ def _medium_alignment(df_query, df_target, tmp_dir, medium_simdf = pd.DataFrame() if len(small_df_query) > 0: small_simdf = _small_alignment( - df_query=small_df_query, df_target=df_target, field_name=field_name + df_query=small_df_query, df_target=df_target, field_name=field_name, + denominator=denominator ) else: small_simdf = pd.DataFrame()