telometer 0.75__tar.gz → 0.76__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {telometer-0.75 → telometer-0.76}/PKG-INFO +1 -1
- {telometer-0.75 → telometer-0.76}/setup.py +1 -1
- {telometer-0.75 → telometer-0.76}/telometer/telometer.py +3 -3
- {telometer-0.75 → telometer-0.76}/telometer.egg-info/PKG-INFO +1 -1
- {telometer-0.75 → telometer-0.76}/LICENSE.txt +0 -0
- {telometer-0.75 → telometer-0.76}/README.md +0 -0
- {telometer-0.75 → telometer-0.76}/setup.cfg +0 -0
- {telometer-0.75 → telometer-0.76}/telometer/__init__.py +0 -0
- {telometer-0.75 → telometer-0.76}/telometer.egg-info/SOURCES.txt +0 -0
- {telometer-0.75 → telometer-0.76}/telometer.egg-info/dependency_links.txt +0 -0
- {telometer-0.75 → telometer-0.76}/telometer.egg-info/entry_points.txt +0 -0
- {telometer-0.75 → telometer-0.76}/telometer.egg-info/top_level.txt +0 -0
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.1
|
|
2
2
|
Name: telometer
|
|
3
|
-
Version: 0.
|
|
3
|
+
Version: 0.76
|
|
4
4
|
Summary: a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data
|
|
5
5
|
Author: Santiago E Sanchez
|
|
6
6
|
Author-email: ses94@stanford.edu
|
|
@@ -2,7 +2,7 @@ import setuptools
|
|
|
2
2
|
|
|
3
3
|
setuptools.setup(
|
|
4
4
|
name="telometer",
|
|
5
|
-
version="0.
|
|
5
|
+
version="0.76",
|
|
6
6
|
author="Santiago E Sanchez",
|
|
7
7
|
author_email="ses94@stanford.edu",
|
|
8
8
|
description="a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data",
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
#!/usr/bin/env python3
|
|
2
|
-
# Telometer v0.
|
|
2
|
+
# Telometer v0.76
|
|
3
3
|
# Created by: Santiago E Sanchez
|
|
4
4
|
# Artandi Lab, Stanford University, 2023
|
|
5
5
|
# Measures telomeres from ONT or PacBio long reads aligned to a T2T genome assembly
|
|
@@ -121,8 +121,8 @@ def calculate_telomere_length():
|
|
|
121
121
|
'reference_name': read.reference_name,
|
|
122
122
|
'mapping_quality': read.mapping_quality,
|
|
123
123
|
'query_sequence': read.query_sequence,
|
|
124
|
-
'reference_length': bam_file.get_reference_length(read.reference_name)
|
|
125
|
-
} for read in bam_file]
|
|
124
|
+
'reference_length': bam_file.get_reference_length(read.reference_name) if read.reference_name is not None else None
|
|
125
|
+
} for read in bam_file if read.reference_name is not None and read.reference_name != 'chrM']
|
|
126
126
|
|
|
127
127
|
with Pool(processes=cpu_count()) as pool:
|
|
128
128
|
results = pool.map(
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.1
|
|
2
2
|
Name: telometer
|
|
3
|
-
Version: 0.
|
|
3
|
+
Version: 0.76
|
|
4
4
|
Summary: a simple regular expression based method for measuring individual, chromosome-specific telomere lengths from long-read sequencing data
|
|
5
5
|
Author: Santiago E Sanchez
|
|
6
6
|
Author-email: ses94@stanford.edu
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|