telometer 0.78__tar.gz → 0.80__tar.gz

{telometer-0.78 → telometer-0.80}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: telometer
-Version: 0.78
+Version: 0.80
 Summary: a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data
 Author: Santiago E Sanchez
 Author-email: ses94@stanford.edu

{telometer-0.78 → telometer-0.80}/setup.py

@@ -2,7 +2,7 @@ import setuptools
 
 setuptools.setup(
     name="telometer",
-    version="0.78",
+    version="0.80",
     author="Santiago E Sanchez",
     author_email="ses94@stanford.edu",
     description="a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data",

{telometer-0.78 → telometer-0.80}/telometer/telometer.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-# Telometer v0.78
+# Telometer v0.79
 # Created by: Santiago E Sanche8
 # Artandi Lab, Stanford University, 2024
 # Measures telomeres from ONT or PacBio long reads aligned to a T2T genome assembly
@@ -88,28 +88,25 @@ def process_read(args):
             telomere_repeat = [m.group() for m in re.finditer(c_rich_telomere_pattern, telomere_region)]
 
         telomere_length = len(''.join(telomere_repeat))
-
+        if telomere_length > 0:
         # Find the region immediately adjacent to the telomere region
-        boundary_mm1_region = seq_to_check[telomere_end:]
-        boundary_mm1_length = find_initial_boundary_region(boundary_mm1_region, g_rich_telomere_pattern.split('|') + c_rich_telomere_pattern.split('|'), max_mismatches=2)
-    else:
-        telomere_start = None
-        telomere_end = None
-        telomere_length = 0
-        boundary_mm1_length = 0
-
-    result = {
-        'read_id': read_data['read_id'],
-        'telomere_start': telomere_start,
-        'telomere_end': telomere_end,
-        'telomere_length': telomere_length,
-        'boundary_mm1_length': boundary_mm1_length,
-        'chromosome': read_data['reference_name'],
-        'mapping_quality': read_data['mapping_quality'],
-        'direction': direction,
-        'arm': arm
-    }
-    return result
+            boundary_mm1_region = seq_to_check[telomere_end:]
+            boundary_mm1_length = find_initial_boundary_region(boundary_mm1_region, g_rich_telomere_pattern.split('|') + c_rich_telomere_pattern.split('|'), max_mismatches=2)
+            result = {
+                'chromosome': read_data['reference_name'],
+                'arm': arm,
+                'telomere_start': telomere_start,
+                'telomere_end': telomere_end,
+                'telomere_length': telomere_length,
+                'subtel_boundary_length': boundary_mm1_length,
+                'read_id': read_data['read_id'],
+                'mapping_quality': read_data['mapping_quality'],
+                'direction': direction
+            }
+            return result
+        else:
+            return None
+
 
 def calculate_telomere_length():
     parser = argparse.ArgumentParser(description='Calculate telomere length from a BAM file.')

{telometer-0.78 → telometer-0.80}/telometer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: telometer
-Version: 0.78
+Version: 0.80
 Summary: a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data
 Author: Santiago E Sanchez
 Author-email: ses94@stanford.edu