telometer 0.74__tar.gz

telometer-0.74/LICENSE.txt

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+Copyright (c) 2024 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

telometer-0.74/PKG-INFO

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+Metadata-Version: 2.1
+Name: telometer
+Version: 0.74
+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
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+License-File: LICENSE.txt
+
+A simple tool for measuring chromosome-specific telomeres from long-read alignments.
+
+[Telometer Github](https://github.com/santiago-es/Telometer) 

telometer-0.74/README.md

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+A simple tool for measuring chromosome-specific telomeres from long-read alignments.
+
+[Telometer Github](https://github.com/santiago-es/Telometer) 

telometer-0.74/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

telometer-0.74/setup.py

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+import setuptools
+
+setuptools.setup(
+    name="telometer",
+    version="0.74",
+    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",
+    packages=setuptools.find_packages(),
+    license='MIT',
+    long_description=open('README.md').read(),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.7',
+    entry_points={
+        'console_scripts': [
+            'telometer=telometer:calculate_telomere_length',  # 'telometer' is the command, 'telometer:main' means the main function in telometer.py
+        ],
+    },
+)

telometer-0.74/telometer/__init__.py

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+from .telometer import calculate_telomere_length
+from .telometer import reverse_complement

telometer-0.74/telometer/telometer.py

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+#!/usr/bin/env python3
+# Telometer v0.74
+# Created by: Santiago E Sanchez
+# Artandi Lab, Stanford University, 2023
+# Measures telomeres from ONT or PacBio long reads aligned to a T2T genome assembly
+# Simple Usage: telometer -b sorted_t2t.bam -o output.tsv
+
+import pysam
+import re
+import regex
+import csv
+import argparse
+import pandas as pd
+
+def reverse_complement(seq):
+    """Returns the reverse complement of a DNA sequence."""
+    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
+    return "".join(complement[base] for base in reversed(seq))
+
+def get_adapters(chemistry):
+    """Returns the adapter sequences based on the sequencing chemistry."""
+    if chemistry == 'r10':
+        adapters = ['TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT', 'GCAATACGTAACTGAACGAAGTACAGG']
+    else:
+        adapters = ['TTTTTTTTTTTAATGTACTTCGTTCAGTTACGTATTGCT', 'GCAATACGTAACTGAACGAAGT']
+
+    adapters_rc = [reverse_complement(adapter) for adapter in adapters]
+    return adapters + adapters_rc
+
+def get_telomere_repeats():
+    """Returns the telomere repeat sequences."""
+    telomere_repeats = ['GGCCA', 'CCCTAA', 'TTAGGG', 'CCCTGG', 'CTTCTT', 'TTAAAA', 'CCTGG']
+    telomere_repeats_rc = [reverse_complement(repeat) for repeat in telomere_repeats]
+    return telomere_repeats + telomere_repeats_rc
+
+def find_initial_boundary_region(sequence, patterns, max_mismatches):
+    """Finds the initial boundary region with allowed mismatches."""
+    boundary_length = 0
+    combined_pattern = '|'.join(f'({pattern})' for pattern in patterns)
+    regex_pattern = f'({combined_pattern}){{2,}}'
+
+    for match in regex.finditer(f'({regex_pattern}){{e<={max_mismatches}}}', sequence, regex.BESTMATCH):
+        boundary_length = max(boundary_length, len(match.group(0)))
+    return boundary_length
+
+def extend_boundary_region(sequence, start, end, patterns, window_size, mismatch_threshold):
+    """Extends the boundary region around the initial match, allowing some mismatches."""
+    extended_start = max(0, start - window_size)
+    extended_end = min(len(sequence), end + window_size)
+    extended_seq = sequence[extended_start:extended_end]
+
+    combined_pattern = ''.join(patterns)
+    mismatches = sum(1 for base in extended_seq if base not in combined_pattern)
+
+    if mismatches / len(extended_seq) <= mismatch_threshold:
+        return len(extended_seq) - (end - start)  # Additional length
+    return 0
+
+def calculate_telomere_length():
+    # required inputs: bam_file_path, output_file_path, chemistry
+    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('-c', '--chemistry', default="r10", help="Sequencing chemistry (r9 or r10, default=r10). Optional", required=False)
+    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)
+    args = parser.parse_args()
+    bam_file = pysam.AlignmentFile(args.bam, "rb")
+
+    adapters = get_adapters(args.chemistry)
+    telomere_repeats = get_telomere_repeats()
+    telomere_repeats_re = "|".join(f'({repeat}){{2,}}' for repeat in telomere_repeats)
+
+    highest_mapping_quality = {}
+    results = []
+    p_count = 0
+    q_count = 0
+    rev_count = 0
+    fwd_count = 0
+    p_tel = 0
+    q_tel = 0
+
+    for read in bam_file:
+        if read.is_unmapped or read.query_sequence is None or len(read.query_sequence) < args.minreadlen:
+            continue
+
+        alignment_start = read.reference_start
+        alignment_end = read.reference_end
+        seq = read.query_sequence
+
+        if read.is_reverse:
+            rev_count += 1
+            direction = "rev"
+            seq = reverse_complement(seq)
+        else:
+            fwd_count += 1
+            direction = "fwd"
+
+        reference_genome_length = bam_file.get_reference_length(read.reference_name)
+
+        if alignment_start < 15000 or alignment_start > reference_genome_length - 30000:
+            if alignment_start < 15000 and "q" not in read.reference_name:
+                arm = "p"
+                p_count += 1
+            else:
+                arm = "q"
+                q_count += 1
+
+            telomere_start = [m.start() for m in re.finditer(telomere_repeats_re, seq)]
+            if telomere_start:
+                telomere_start = telomere_start[0]
+                if telomere_start > 100 and (len(seq) - telomere_start > 200):
+                    continue
+
+                telomere_end = min((seq.find(adapter) for adapter in adapters), default=-1)
+                if telomere_end == -1:
+                    telomere_end = len(seq)
+
+                telomere_region = seq[telomere_start:telomere_end]
+                telomere_repeat = [m.group() for m in re.finditer('|'.join(telomere_repeats), telomere_region)]
+                telomere_length = len(''.join(telomere_repeat))
+
+                boundary_mm1_length = find_initial_boundary_region(telomere_region, telomere_repeats, max_mismatches=1)
+
+                if telomere_length < boundary_mm1_length:
+                    telomere_length = boundary_mm1_length
+                if telomere_length < boundary_mm2_length:
+                    telomere_length = boundary_mm2_length
+
+                if read.query_name not in highest_mapping_quality or read.mapping_quality > highest_mapping_quality[read.query_name]:
+                    if arm == "p":
+                        p_tel += 1
+                    else:
+                        q_tel += 1
+                    highest_mapping_quality[read.query_name] = read.mapping_quality
+                    results.append({
+                        'chromosome': read.reference_name,
+                        'reference_start': alignment_start,
+                        'reference_end': alignment_end,
+                        'telomere_length': telomere_length,
+                        'subtel_boundary_length': boundary_mm1_length,
+                        'read_id': read.query_name,
+                        'mapping_quality': read.mapping_quality,
+                        'read_length': len(seq),
+                        'arm': arm,
+                        'direction': direction
+                    })
+
+    bam_file.close()
+
+    with open(args.output, 'w', newline='') as output_file:
+        writer = csv.DictWriter(output_file, fieldnames=results[0].keys(), delimiter='\t')
+        writer.writeheader()
+        writer.writerows(results)
+
+    # Print the total number of telomeres measured
+    print(f"Telometer completed successfully. Total telomeres measured: {len(results)}")
+
+if __name__ == "__main__":
+    calculate_telomere_length()

telometer-0.74/telometer.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: telometer
+Version: 0.74
+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
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+License-File: LICENSE.txt
+
+A simple tool for measuring chromosome-specific telomeres from long-read alignments.
+
+[Telometer Github](https://github.com/santiago-es/Telometer) 

telometer-0.74/telometer.egg-info/SOURCES.txt

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+LICENSE.txt
+README.md
+setup.py
+telometer/__init__.py
+telometer/telometer.py
+telometer.egg-info/PKG-INFO
+telometer.egg-info/SOURCES.txt
+telometer.egg-info/dependency_links.txt
+telometer.egg-info/entry_points.txt
+telometer.egg-info/top_level.txt

telometer-0.74/telometer.egg-info/dependency_links.txt

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+

telometer-0.74/telometer.egg-info/entry_points.txt

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+[console_scripts]
+telometer = telometer:calculate_telomere_length

telometer-0.74/telometer.egg-info/top_level.txt

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+telometer