Make query sequence logging less verbose in MSA tools

PiperOrigin-RevId: 775647191
Change-Id: I3804586da51525b58c98a91c400523cda160eaf7
This commit is contained in:
Augustin Zidek
2025-06-25 05:35:39 -07:00
committed by Copybara-Service
parent 6cf825575b
commit 53d2acc5b7
2 changed files with 13 additions and 2 deletions

View File

@ -75,7 +75,13 @@ class Jackhmmer(msa_tool.MsaTool):
def query(self, target_sequence: str) -> msa_tool.MsaToolResult:
"""Queries the database using Jackhmmer."""
logging.info('Query sequence: %s', target_sequence)
logging.info(
'Query sequence: %s',
target_sequence
if len(target_sequence) <= 16
else f'{target_sequence[:16]}... (len {len(target_sequence)})',
)
with tempfile.TemporaryDirectory() as query_tmp_dir:
input_fasta_path = os.path.join(query_tmp_dir, 'query.fasta')
subprocess_utils.create_query_fasta_file(

View File

@ -85,7 +85,12 @@ class Nhmmer(msa_tool.MsaTool):
def query(self, target_sequence: str) -> msa_tool.MsaToolResult:
"""Query the database using Nhmmer."""
logging.info('Query sequence: %s', target_sequence)
logging.info(
'Query sequence: %s',
target_sequence
if len(target_sequence) <= 16
else f'{target_sequence[:16]}... (len {len(target_sequence)})',
)
with tempfile.TemporaryDirectory() as query_tmp_dir:
input_a3m_path = os.path.join(query_tmp_dir, 'query.a3m')