telometer 0.93__tar.gz → 0.94__tar.gz

{telometer-0.93 → telometer-0.94}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: telometer
-Version: 0.93
+Version: 0.94
 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-0.93 → telometer-0.94}/setup.py

@@ -2,7 +2,7 @@ import setuptools
 
 setuptools.setup(
     name="telometer",
-    version="0.93",
+    version="0.94",
     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",
@@ -17,7 +17,7 @@ setuptools.setup(
     python_requires='>=3.7',
     entry_points={
         'console_scripts': [
-            'telometer=telometer:process_bam_file',  # 'telometer' is the command, 'telometer:main' means the main function in telometer.py
+            'telometer=telometer:run_telometer',  # 'telometer' is the command, 'telometer:main' means the main function in telometer.py
         ],
     },
 )

{telometer-0.93 → telometer-0.94}/telometer/__init__.py

@@ -12,7 +12,8 @@ from .telometer import (
     get_telomere_repeats,
     reverse_complement,
     process_read_wrapper,
-    process_read
+    process_read,
+    run_telometer
 )
 
 

{telometer-0.93 → telometer-0.94}/telometer/telometer.py

@@ -9,6 +9,7 @@ import pysam
 import regex as re
 import pandas as pd
 import time
+import argparse
 from multiprocessing import Pool, cpu_count
 
 
@@ -192,16 +193,15 @@ def process_bam_file(bam_file_path, output_file_path, max_gap_length=100, min_re
     print(f"Telometer completed successfully. Total telomeres measured: {len(read_results)}")
     print(f"Total processing time: {time.time() - start_time:.2f} seconds")
 
-if __name__ == "__main__":
-    import argparse
-
+def run_telometer:
     parser = argparse.ArgumentParser(description='Calculate telomere length from a BAM file.')
     parser.add_argument('-b', '--bam', help='The path to the sorted BAM file.', required=True)
     parser.add_argument('-o', '--output', help='The path to the output file.', required=True)
     parser.add_argument('-m', '--minreadlen', default=1000, type=int, help='Minimum read length to consider (Default: 1000 for telomere capture, use 4000 for WGS). Optional', required=False)
     parser.add_argument('-g', '--maxgaplen', default=100, type=int, help='Maximum allowed gap length between telomere regions. Optional', required=False)
     parser.add_argument('-t', '--threads', default=cpu_count(), type=int, help='Number of processing threads to use. Optional', required=False)
-
     args = parser.parse_args()
-
     process_bam_file(args.bam, args.output, max_gap_length=args.maxgaplen, min_read_len=args.minreadlen, num_processes=args.threads)
+
+if __name__ == "__main__":
+    run_telometer()

{telometer-0.93 → telometer-0.94}/telometer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: telometer
-Version: 0.93
+Version: 0.94
 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-0.94/telometer.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+telometer = telometer:run_telometer

telometer-0.93/telometer.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-telometer = telometer:process_bam_file