adding logging to io.genomio.fasta.process

src/python/ensembl/io/genomio/fasta/process.py

@@ -23,8 +23,13 @@
 from Bio import SeqIO
 
 from ensembl.io.genomio.utils.archive_utils import open_gz_file
+from ensembl.io.genomio.utils.logging import setup_logging
 from ensembl.utils.argparse import ArgumentParser
 
+# logging references module, but can be overridden by a specific logger
+import logging
+logger = logging # by default
+
 
 exclude_seq_regions: List[str] = []
 
@@ -41,13 +46,14 @@ def get_peptides_to_exclude(genbank_path: PathLike, seqr_to_exclude: Set[str]) -
     with open_gz_file(genbank_path) as in_genbank:
         for record in SeqIO.parse(in_genbank, "genbank"):
             if record.id in seqr_to_exclude:
-                print(f"Skip sequence {record.id}")
+                logger.info(f"Skip sequence {record.id}")
                 for feat in record.features:
                     if feat.type == "CDS":
                         if "protein_id" in feat.qualifiers:
                             feat_id = feat.qualifiers["protein_id"]
                             peptides_to_exclude.add(feat_id[0])
                         else:
+                            logger.critical(f"Peptide without peptide ID ${feat}")
                             raise GFFParserError(f"Peptide without peptide ID ${feat}")
     return peptides_to_exclude
 
@@ -82,7 +88,7 @@ def prep_fasta_data(
     with open_gz_file(file_path) as in_fasta:
         for record in SeqIO.parse(in_fasta, "fasta"):
             if record.id in to_exclude:
-                print(f"Skip record ${record.id}")
+                logger.info(f"Skip record ${record.id}")
             else:
                 records.append(record)
     with Path(fasta_outfile).open("w") as out_fasta:
@@ -96,6 +102,11 @@ def main() -> None:
     parser.add_argument_src_path("--genbank_infile", help="Input GenBank GBFF file")
     parser.add_argument_dst_path("--fasta_outfile", required=True, help="Output FASTA file")
     parser.add_argument("--peptide_mode", action="store_true", help="Process proteins instead of DNA")
+    parser.add_argument("-v", "--verbose", action="store_true", help="Verbose level logging")
+    parser.add_argument("-d", "--debug", action="store_true", help="Debug level logging")
+    parser.add_argument("-l", "--logfile", required=False, type=str, help="file to log to")
     args = parser.parse_args()
 
+    logger = setup_logging(args, name = __name__)
+
     prep_fasta_data(**vars(args))

src/python/ensembl/io/genomio/utils/__init__.py

@@ -16,3 +16,4 @@
 
 from .archive_utils import *
 from .json_utils import *
+from .logging import *

src/python/ensembl/io/genomio/utils/logging.py

@@ -0,0 +1,79 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Utils to deal with logging."""
+
+__all__ = ["setup_logging"]
+
+import argparse
+import logging
+from typing import Optional
+
+
+# default logging formats
+LOGGING_FORMAT = "%(asctime)s\t%(levelname)s\t%(message)s"
+DATE_FORMAT = r"%Y-%m-%d_%H:%M:%S"
+
+# helper functions
+def _prepare_console_handler(*, debug: bool = False, verbose: bool = False) -> logging.StreamHandler:
+    """setup console handler with different logging levels"""
+    console_h = logging.StreamHandler()
+    # set default logging level
+    if debug:
+        console_h.setLevel(logging.DEBUG)
+    elif verbose:
+        console_h.setLevel(logging.INFO)
+    return console_h
+
+
+def _prepare_file_handler(filename: Optional[str] = None, *, debug: bool = False) -> Optional[logging.FileHandler]:
+    """setup file handler with default loggin.INFO level"""
+    """retuns None if no file name defined"""
+    if filename is None:
+        return None
+
+    file_h = logging.FileHandler(filename)
+
+    file_h.setLevel(logging.INFO)
+    if debug:
+        file_h.setLevel(logging.DEBUG)
+
+    return file_h
+
+
+def setup_logging(
+        args: argparse.Namespace,
+        *, # no positional arguments allowed after this
+        name: Optional[str] = None,
+    ) -> logging.Logger:
+    """Setup logging infrustucture."""
+    """args: argparse.Namespace -- args with "debug", "verbose" and "logfile" options."""
+    # get logger with a specified name (or the default one)
+    logger = logging.getLogger(name)
+
+    # set up shared formatter
+    formatter = logging.Formatter(fmt = LOGGING_FORMAT, datefmt = DATE_FORMAT)
+
+    # adding console handler
+    console_h = _prepare_console_handler(debug = args.debug, verbose = args.verbose)
+    console_h.setFormatter(formatter)
+    logger.addHandler(console_h)
+
+    # adding logging to file
+    file_h = _prepare_file_handler(args.logfile)
+    if file_h:
+        file_h.setFormatter(formatter)
+        logger.addHandler(file_h)
+
+    return logger