refactor: update logging level (#171)

* refactor: update logging levels * revert rounding * refactor: minor fixes to logging --------- Co-authored-by: Alex Kanitz <[email protected]>
zavolanlab · Oct 30, 2024 · 797abe8 · 797abe8
1 parent ef82690
commit 797abe8
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Showing 5 changed files with 29 additions and 25 deletions.
diff --git a/htsinfer/get_library_source.py b/htsinfer/get_library_source.py
@@ -83,7 +83,10 @@ def evaluate(self) -> ResultsSource:
                 self.transcripts_file
             )
             source.file_1.short_name = src_name
-
+            LOGGER.info(
+                f'Library source taxonomy ID: {self.tax_id}, '
+                f'short name: {source.file_1.short_name}'
+            )
             if self.paths[1] is not None:
                 source.file_2.taxon_id = self.tax_id
                 source.file_2.short_name = source.file_1.short_name
@@ -211,7 +214,7 @@ def run_kallisto_quantification(
         Raises:
             KallistoProblem: Kallisto quantification failed.
         """
-        LOGGER.debug(f"Running Kallisto quantification for: {fastq}")
+        LOGGER.info(f"Running Kallisto quantification for: {fastq}")
 
         with tempfile.TemporaryDirectory(
             prefix="kallisto_",

diff --git a/htsinfer/get_library_stats.py b/htsinfer/get_library_stats.py
@@ -60,8 +60,8 @@ def evaluate(self) -> ResultsStats:
             self.fastq_get_stats_read_length(fastq=self.paths[0])
         )
         # process file 2
-        LOGGER.info(f"Obtaining statistics for file: {self.paths[1]}")
         if self.paths[1] is not None:
+            LOGGER.info(f"Obtaining statistics for file: {self.paths[1]}")
             (stats.file_2.read_length.min,
              stats.file_2.read_length.max,
              stats.file_2.read_length.mean,
@@ -88,7 +88,8 @@ def fastq_get_stats_read_length(fastq: Path) -> Tuple[
             FileProblem: Could not process FASTQ file.
         """
         LOGGER.debug(
-            f"Extracting read length statistics in: {fastq}")
+            f"Extracting read length statistics in: {fastq}"
+        )
         min_len: int = 1000000
         max_len: int = 0
         total_lengths: int = 0

diff --git a/htsinfer/get_library_type.py b/htsinfer/get_library_type.py
@@ -135,7 +135,7 @@ def _evaluate_mate_relationship(
                 self.library_source.file_1.short_name is not None or
                 self.library_source.file_2.short_name is not None
             ):
-                LOGGER.debug("Determining mate relationship by alignment...")
+                LOGGER.info("Determining mate relationship by alignment...")
                 self.mapping.library_type.relationship \
                     = StatesTypeRelationship.not_available
                 self.mapping.library_source = self.library_source
@@ -146,7 +146,7 @@ def _evaluate_mate_relationship(
             self.library_source.file_1.short_name is not None or
             self.library_source.file_2.short_name is not None
         ):
-            LOGGER.debug("Determining mate relationship by alignment...")
+            LOGGER.info("Determining mate relationship by alignment...")
             self.mapping.library_type.relationship \
                 = StatesTypeRelationship.not_available
             self.mapping.library_source = self.library_source
@@ -155,7 +155,7 @@ def _evaluate_mate_relationship(
             self._align_mates()
         else:
             self.results.relationship = StatesTypeRelationship.not_available
-            LOGGER.debug(
+            LOGGER.info(
                 "Sequence IDs and library source are not determined, "
                 "mate relationship cannot be inferred."
             )
@@ -220,9 +220,9 @@ def _align_mates(self):
         aligned_mate1 = len(list(filter(None, mate1)))
         aligned_mate2 = len(list(filter(None, mate2)))
 
-        LOGGER.debug(f"Number of aligned reads file 1: {aligned_mate1}")
-        LOGGER.debug(f"Number of aligned reads file 2: {aligned_mate2}")
-        LOGGER.debug(f"Number of concordant reads: {concordant}")
+        LOGGER.info(f"Number of aligned reads file 1: {aligned_mate1}")
+        LOGGER.info(f"Number of aligned reads file 2: {aligned_mate2}")
+        LOGGER.info(f"Number of concordant reads: {concordant}")
 
         self._update_relationship_type(
             concordant, min(aligned_mate1, aligned_mate2)
@@ -351,7 +351,7 @@ def evaluate(self) -> None:
             with open(self.path, encoding="utf-8") as _f:  # type: ignore
 
                 # Get sequence identifier format from first record
-                LOGGER.debug(
+                LOGGER.info(
                     "Determining identifier and library type from first "
                     "record..."
                 )
@@ -375,13 +375,13 @@ def evaluate(self) -> None:
                     raise FileProblem(f"File is empty: {self.path}") from exc
 
                 if self.seq_id_format is not None:
-                    LOGGER.debug(
+                    LOGGER.info(
                         "Sequence identifier format: "
                         f"{self.seq_id_format.name}"
                     )
                 else:
                     self.result = StatesType.not_available
-                    LOGGER.debug(
+                    LOGGER.info(
                         "Could not determine sequence identifier format."
                     )
 

diff --git a/htsinfer/get_read_orientation.py b/htsinfer/get_read_orientation.py
@@ -81,7 +81,7 @@ def evaluate(self) -> ResultsOrientation:
             self.library_source.file_1.short_name is not None or
             self.library_source.file_2.short_name is not None
         ):
-            LOGGER.debug("Determining read relationship by alignment...")
+            LOGGER.info("Determining read relationship by alignment...")
             self.mapping.evaluate()
 
         return self.process_alignments(star_dirs=self.mapping.star_dirs)
@@ -155,7 +155,7 @@ def process_single(
                 f"Failed to open SAM file: '{sam}'"
             ) from exc
 
-        LOGGER.debug("Deciding read orientation...")
+        LOGGER.info("Deciding read orientation...")
         reads = len(states)
         fractions = [
             self.get_frequencies(*state) for state in states.values()
@@ -182,12 +182,12 @@ def process_single(
             reads, fractions_all_states, orientation, paired=False
         )
 
-        LOGGER.debug(
+        LOGGER.info(
             f"Required number of mapped reads: {self.min_mapped_reads}"
         )
-        LOGGER.debug(f"Number of mapped reads: {orient_df.iloc[0, 0]}")
-        LOGGER.debug(f"Fraction of SF: {orient_df.iloc[0, 1]}")
-        LOGGER.debug(f"Fraction of SR: {orient_df.iloc[0, 2]}")
+        LOGGER.info(f"Number of mapped reads: {orient_df.iloc[0, 0]}")
+        LOGGER.info(f"Fraction of SF: {orient_df.iloc[0, 1]}")
+        LOGGER.info(f"Fraction of SR: {orient_df.iloc[0, 2]}")
         LOGGER.debug(f"Orientation: {orient_df.iloc[0, 3]}")
 
         self.write_orientation_to_json(orient_df, self.paths[0].name)
@@ -268,7 +268,7 @@ def process_paired(  # pylint: disable=R0912,R0915
             ) from exc
 
         # deciding read orientation
-        LOGGER.debug("Deciding read orientation...")
+        LOGGER.info("Deciding read orientation...")
         reads = len(states)
         fractions = [
             self.get_frequencies(*state) for state in states.values()
@@ -309,12 +309,12 @@ def process_paired(  # pylint: disable=R0912,R0915
             reads, fractions_all_states, orientation, paired=True, file_index=2
         )
 
-        LOGGER.debug(
+        LOGGER.info(
             f"Required number of mapped reads: {self.min_mapped_reads}"
         )
-        LOGGER.debug(f"Number of mapped reads: {orient_df_1.iloc[0, 0]}")
-        LOGGER.debug(f"Fraction of ISF: {orient_df_1.iloc[0, 1]}")
-        LOGGER.debug(f"Fraction of ISR: {orient_df_1.iloc[0, 2]}")
+        LOGGER.info(f"Number of mapped reads: {orient_df_1.iloc[0, 0]}")
+        LOGGER.info(f"Fraction of ISF: {orient_df_1.iloc[0, 1]}")
+        LOGGER.info(f"Fraction of ISR: {orient_df_1.iloc[0, 2]}")
         LOGGER.debug(f"Orientation file 1: {orient_df_1.iloc[0, 3]}")
         LOGGER.debug(f"Orientation file 2: {orient_df_2.iloc[0, 3]}")
         LOGGER.debug(

diff --git a/htsinfer/mapping.py b/htsinfer/mapping.py
@@ -355,7 +355,7 @@ def generate_star_alignments(commands: Dict[Path, List[str]]) -> None:
         Raises:
             StarProblem: Generating alignments failed.
         """
-        LOGGER.debug("Aligning reads with STAR...")
+        LOGGER.info("Aligning reads with STAR...")
 
         # execute commands
         for out_dir, cmd in commands.items():