From 0bcc152d9678cf1298b0eace3c83f87b1eb7f0d6 Mon Sep 17 00:00:00 2001
From: balajtimate <balajtimate@gmail.com>
Date: Thu, 3 Oct 2024 17:04:20 +0200
Subject: [PATCH] feat: add read orient paired json output

---
 htsinfer/get_read_orientation.py | 58 +++++++++++++++++++++++++++++---
 1 file changed, 53 insertions(+), 5 deletions(-)

diff --git a/htsinfer/get_read_orientation.py b/htsinfer/get_read_orientation.py
index 01a0c9b..3ad298e 100644
--- a/htsinfer/get_read_orientation.py
+++ b/htsinfer/get_read_orientation.py
@@ -319,13 +319,61 @@ def process_paired(  # pylint: disable=R0912,R0915
                 orientation.file_1 = StatesOrientation.unstranded
                 orientation.file_2 = StatesOrientation.unstranded
 
-        # write log messages and return result
+        orient_df_1 = pd.DataFrame([{
+            'Number of mapped reads': reads,
+            'Fraction ISF': fractions_all_states.get(
+                StatesOrientationRelationship.inward_stranded_forward
+            ),
+            'Fraction ISR': fractions_all_states.get(
+                StatesOrientationRelationship.inward_stranded_reverse
+            ),
+            'Orientation': getattr(orientation.file_1, 'value', None),
+            'Relationship': getattr(orientation.relationship, 'value', None)
+        }])
+        orient_df_2 = pd.DataFrame([{
+            'Number of mapped reads': reads,
+            'Fraction ISF': fractions_all_states.get(
+                StatesOrientationRelationship.inward_stranded_forward
+            ),
+            'Fraction ISR': fractions_all_states.get(
+                StatesOrientationRelationship.inward_stranded_reverse
+            ),
+            'Orientation': getattr(orientation.file_2, 'value', None),
+            'Relationship': getattr(orientation.relationship, 'value', None)
+        }])
+        LOGGER.debug(
+            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.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(
-            f"Required number of mapped read pairs: {self.min_mapped_reads}"
+            f"Orientation relationship: {orient_df_1.iloc[0, 4]}"
         )
-        LOGGER.debug(f"Number of reads mapped: {reads}")
-        LOGGER.debug(f"Fraction of states: {fractions_all_states}")
-        LOGGER.debug(f"Orientation: {orientation}")
+        filename_1 = (
+            Path(self.out_dir) / f"read_orientation_{self.paths[0].name}.json"
+        )
+        LOGGER.debug(f"Writing results to file: {filename_1}")
+        orient_df_1.to_json(
+            filename_1,
+            orient='split',
+            index=False,
+            indent=True,
+        )
+        filename_2 = (
+            Path(self.out_dir) / f"read_orientation_"
+            f"{getattr(self.paths[1], 'name')}.json"
+        )
+        LOGGER.debug(f"Writing results to file: {filename_2}")
+        orient_df_2.to_json(
+            filename_2,
+            orient='split',
+            index=False,
+            indent=True,
+        )
+
         return orientation
 
     @staticmethod