From d1326ecd2a634110058aedcc6941cd788efb68d3 Mon Sep 17 00:00:00 2001
From: ZL Deng <dawnmsg@gmail.com>
Date: Thu, 21 Dec 2023 23:47:38 +0100
Subject: [PATCH] Fix logging issue for paired-end reads input

---
 ribodetector/__init__.py          | 2 +-
 ribodetector/detect.py            | 6 ++++--
 ribodetector/detect_cpu.py        | 6 +++---
 ribodetector/utils/__version__.py | 2 +-
 setup.py                          | 2 +-
 5 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/ribodetector/__init__.py b/ribodetector/__init__.py
index 4c45ff8..c41d965 100644
--- a/ribodetector/__init__.py
+++ b/ribodetector/__init__.py
@@ -4,5 +4,5 @@
 Accurate and rapid RiboRNA sequences Detector based on deep learning.
 """
 
-__version__ = "0.2.9"
+__version__ = "0.3.0"
 __author__ = 'ZL Deng'
diff --git a/ribodetector/detect.py b/ribodetector/detect.py
index b08a7b6..2b9dfe6 100644
--- a/ribodetector/detect.py
+++ b/ribodetector/detect.py
@@ -59,7 +59,7 @@ def get_state_dict(self):
             #                 "Sequence length must be set to larger than 40.")
 
             self.logger.info(
-                'The accuracy will be low with reads shorter than 40.')
+                'The accuracy will drop with reads shorter than 40.')
 
         # High recall model if ensure non-rRNA
         if self.args.ensure == 'norrna':
@@ -447,7 +447,9 @@ def run_with_chunks(self):
         else:
             if self.rrna is not None:
                 self.logger.info('Writing output rRNA sequences into file: {}{}{}'.format(
-                    colors.OKBLUE, ", ".join(self.rrna), colors.ENDC))
+                    colors.OKBLUE, 
+                    ", ".join(self.rrna), 
+                    colors.ENDC))
                 rrna_fh = open_for_write(self.rrna[0])
                 #num_rrna = 0
 
diff --git a/ribodetector/detect_cpu.py b/ribodetector/detect_cpu.py
index b7a20f7..91191cb 100644
--- a/ribodetector/detect_cpu.py
+++ b/ribodetector/detect_cpu.py
@@ -60,7 +60,7 @@ def load_model(self):
             #             raise RuntimeError(
             #                 "Sequence length must be set to larger than 40.")
             self.logger.info(
-                'The accuracy will be low with reads shorter than 40.')
+                'The accuracy will drop with reads shorter than 40.')
 
         # High recall model if ensure non-rRNA
         if self.args.ensure == 'norrna':
@@ -432,7 +432,7 @@ def run_with_chunks(self):
                         # del r1_data, r2_data, r1_output, r2_output, r1_batch_labels, r2_batch_labels
                 num_read += len(chunk[0])
 
-                self.logger.info('{}{}{}{} reads finished!'.format(
+                self.logger.info('{}{}{} sequences finished!'.format(
                     colors.OKGREEN,
                     num_read,
                     colors.ENDC))
@@ -535,7 +535,7 @@ def run_with_chunks(self):
 
                 num_read += len(chunk)
 
-                self.logger.info('{}{}{} reads finished!'.format(
+                self.logger.info('{}{}{} sequences finished!'.format(
                     colors.OKGREEN,
                     num_read,
                     colors.ENDC))
diff --git a/ribodetector/utils/__version__.py b/ribodetector/utils/__version__.py
index cd9b137..0404d81 100644
--- a/ribodetector/utils/__version__.py
+++ b/ribodetector/utils/__version__.py
@@ -1 +1 @@
-__version__ = '0.2.9'
+__version__ = '0.3.0'
diff --git a/setup.py b/setup.py
index 512b1b4..250581d 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
 
 setup(
     name="ribodetector",
-    version="0.2.9",
+    version="0.3.0",
     python_requires=">=3.8, <=3.10",
     author="Z-L Deng",
     author_email="dawnmsg@gmail.com",