refactor: minor fixes to logging

zavolanlab · Oct 30, 2024 · ac71324 · ac71324
1 parent fb23e09
commit ac71324
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 6 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

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,

diff --git a/htsinfer/get_read_orientation.py b/htsinfer/get_read_orientation.py
@@ -186,8 +186,8 @@ def process_single(
             f"Required number of mapped reads: {self.min_mapped_reads}"
         )
         LOGGER.info(f"Number of mapped reads: {orient_df.iloc[0, 0]}")
-        LOGGER.info(f"Fraction of SF: {orient_df.iloc[0, 1], 3}")
-        LOGGER.info(f"Fraction of SR: {orient_df.iloc[0, 2], 3}")
+        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)
@@ -313,8 +313,8 @@ def process_paired(  # pylint: disable=R0912,R0915
             f"Required number of mapped reads: {self.min_mapped_reads}"
         )
         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], 3}")
-        LOGGER.info(f"Fraction of ISR: {orient_df_1.iloc[0, 2], 3}")
+        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(